@article{thevenot_analysis_2015,
	title = {Analysis of the Human Adult Urinary Metabolome Variations with Age, Body Mass Index, and Gender by Implementing a Comprehensive Workflow for Univariate and OPLS Statistical Analyses},
	author = {Thevenot},
	year = {2015}
}


@article{liaw_classication_2002,
	title = {Classiﬁcation and {Regression} by {randomForest}},
	volume = {2},
	language = {en},
	author = {Liaw, Andy and Wiener, Matthew},
	year = {2002},
	pages = {6},
	file = {Liaw et Wiener - 2002 - Classiﬁcation and Regression by randomForest.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\E5XXJQ47\\Liaw et Wiener - 2002 - Classiﬁcation and Regression by randomForest.pdf:application/pdf}
}

@article{guyon_gene_nodate,
	title = {Gene {Selection} for {Cancer} {Classification} using {Support} {Vector} {Machines}},
	abstract = {DNA micro-arrays now permit scientists to screen thousands of genes simultaneously and determine whether those genes are active, hyperactive or silent in normal or cancerous tissue. Because these new micro-array devices generate bewildering amounts of raw data, new analytical methods must be developed to sort out whether cancer tissues have distinctive signatures of gene expression over normal tissues or other types of cancer tissues. In this paper, we address the problem of selection of a small subset of genes from broad patterns of gene expression data, recorded on DNA micro-arrays. Using available training examples from cancer and normal patients, we build a classiﬁer suitable for genetic diagnosis, as well as drug discovery. Previous attempts to address this problem select genes with correlation techniques. We propose a new method of gene selection utilizing Support Vector Machine methods based on Recursive Feature Elimination (RFE). We demonstrate experimentally that the genes selected by our techniques yield better classiﬁcation performance and are biologically relevant to cancer.},
	language = {en},
	author = {Guyon, Isabelle and Weston, Jason and Barnhill, Stephen},
	pages = {34},
	file = {Guyon et al. - Gene Selection for Cancer Classification using Sup.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\7UB8BQW3\\Guyon et al. - Gene Selection for Cancer Classification using Sup.pdf:application/pdf}
}

@article{abdi_metric_nodate,
	title = {Metric {Multidimensional} {Scaling} ({MDS}): {Analyzing} {Distance} {Matrices}},
	language = {en},
	author = {Abdi, Hervé},
	pages = {13},
	file = {Abdi - Metric Multidimensional Scaling (MDS) Analyzing D.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\2CAYX3ZZ\\Abdi - Metric Multidimensional Scaling (MDS) Analyzing D.pdf:application/pdf}
}

@article{wold_pls-regression:_2001,
	title = {{PLS}-regression: a basic tool of chemometrics},
	volume = {58},
	issn = {01697439},
	shorttitle = {{PLS}-regression},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0169743901001551},
	doi = {10.1016/S0169-7439(01)00155-1},
	abstract = {PLS-regression ŽPLSR. is the PLS approach in its simplest, and in chemistry and technology, most used form Žtwo-block predictive PLS.. PLSR is a method for relating two data matrices, X and Y, by a linear multivariate model, but goes beyond traditional regression in that it models also the structure of X and Y. PLSR derives its usefulness from its ability to analyze data with many, noisy, collinear, and even incomplete variables in both X and Y. PLSR has the desirable property that the precision of the model parameters improves with the increasing number of relevant variables and observations.},
	language = {en},
	number = {2},
	urldate = {2019-01-31},
	journal = {Chemometrics and Intelligent Laboratory Systems},
	author = {Wold, Svante and Sjöström, Michael and Eriksson, Lennart},
	month = oct,
	year = {2001},
	pages = {109--130},
	file = {Wold et al. - 2001 - PLS-regression a basic tool of chemometrics.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\X954P7LY\\Wold et al. - 2001 - PLS-regression a basic tool of chemometrics.pdf:application/pdf}
}

@article{granitto_recursive_2006,
	title = {Recursive feature elimination with random forest for {PTR}-{MS} analysis of agroindustrial products},
	volume = {83},
	issn = {01697439},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0169743906000232},
	doi = {10.1016/j.chemolab.2006.01.007},
	abstract = {In this paper we apply the recently introduced Random Forest-Recursive Feature Elimination (RF-RFE) algorithm to the identification of relevant features in the spectra produced by Proton Transfer Reaction-Mass Spectrometry (PTR-MS) analysis of agroindustrial products. The method is compared with the more traditional Support Vector Machine-Recursive Feature Elimination (SVM-RFE), extended to allow multiclass problems, and with a baseline method based on the Kruskal–Wallis statistic (KWS). In particular, we apply all selection methods to the discrimination of nine varieties of strawberries and six varieties of typical cheeses from Trentino Province, North Italy. Using replicated experiments we estimate unbiased generalization errors. Our results show that RF-RFE outperforms SVM-RFE and KWS on the task of finding small subsets of features with high discrimination levels on PTR-MS data sets. We also show how selection probabilities and features cooccurrence can be used to highlight the most relevant features for discrimination.},
	language = {en},
	number = {2},
	urldate = {2019-01-31},
	journal = {Chemometrics and Intelligent Laboratory Systems},
	author = {Granitto, Pablo M. and Furlanello, Cesare and Biasioli, Franco and Gasperi, Flavia},
	month = sep,
	year = {2006},
	pages = {83--90},
	file = {Granitto et al. - 2006 - Recursive feature elimination with random forest f.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\9RPYQ4RI\\Granitto et al. - 2006 - Recursive feature elimination with random forest f.pdf:application/pdf}
}

@article{seoane_using_2014,
	title = {Using a {Random} {Forest} proximity measure for variable importance stratification in genotypic data},
	abstract = {In this work we study variable-significance in classification using the Random Forest proximity matrix and local Importance matrix. We use the proximity m atrix t o g roup t he s amples acr oss a num ber of c lusters a nd use t hese clusters to s tratify th e importance of a v ariable. W e apply t his a pproach t o a cardiovascular g enotype d ataset f or sample classification b ased o n coronary heart disease and we found a number of variations related with cardiovascular disease phenotypes. We also used a set of phenotypes related with this genotype data to match the obtained clusters with coronary heart diseases phenotypes.},
	language = {en},
	author = {Seoane, Jose A and Day, Ian N M and Campbell, Colin and Casas, Juan P and Gaunt, Tom R},
	year = {2014},
	pages = {12},
	file = {Seoane et al. - 2014 - Using a Random Forest proximity measure for variab.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\GIZXCXST\\Seoane et al. - 2014 - Using a Random Forest proximity measure for variab.pdf:application/pdf}
}

@article{cappellin_linking_2012,
	title = {Linking {GC}-{MS} and {PTR}-{TOF}-{MS} fingerprints of food samples},
	volume = {118},
	issn = {01697439},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0169743912001219},
	doi = {10.1016/j.chemolab.2012.05.008},
	abstract = {Recently the ﬁrst applications in food science and technology of the newly available volatile organic compound (VOC) detection technique proton transfer reaction‐mass spectrometry, coupled with a time of ﬂight mass analyzer (PTR-TOF-MS), have been published. In comparison with standard techniques such as GC-MS, PTR-TOF-MS has the remarkable advantage of being extremely fast but has the drawback that compound identiﬁcation is more challenging and often not possible without further information. In order to better exploit and understand the analytical information entangled in the PTR-TOF-MS ﬁngerprint and to link it with SPME/GC-MS analyses we employed two multivariate calibration methods, PLS and the more recent LASSO. We show that, while in some cases it is sufﬁcient to consider a single PTR-TOF-MS peak in order to predict the intensity of a SPME/GC-MS peak, in general a multivariate approach is needed. We compare the performances of PLS and LASSO in terms of prediction capabilities and interpretability of the model coefﬁcients and conclude that LASSO is more suitable for this problem. As case study, we compared GC and PTR-MS data for different matrices, namely olive oil and grana cheese.},
	language = {en},
	urldate = {2019-01-31},
	journal = {Chemometrics and Intelligent Laboratory Systems},
	author = {Cappellin, Luca and Aprea, Eugenio and Granitto, Pablo and Wehrens, Ron and Soukoulis, Christos and Viola, Roberto and Märk, Tilmann D. and Gasperi, Flavia and Biasioli, Franco},
	month = aug,
	year = {2012},
	pages = {301--307},
	file = {Cappellin et al. - 2012 - Linking GC-MS and PTR-TOF-MS fingerprints of food .pdf:C\:\\Users\\CR258086\\Zotero\\storage\\W9H59WFJ\\Cappellin et al. - 2012 - Linking GC-MS and PTR-TOF-MS fingerprints of food .pdf:application/pdf}
}

@article{cappellin_extending_2011,
	title = {Extending the dynamic range of proton transfer reaction time-of-flight mass spectrometers by a novel dead time correction},
	volume = {25},
	issn = {09514198},
	url = {http://doi.wiley.com/10.1002/rcm.4819},
	doi = {10.1002/rcm.4819},
	language = {en},
	number = {1},
	urldate = {2019-01-31},
	journal = {Rapid Communications in Mass Spectrometry},
	author = {Cappellin, Luca and Biasioli, Franco and Schuhfried, Erna and Soukoulis, Christos and Märk, Tilmann D. and Gasperi, Flavia},
	month = jan,
	year = {2011},
	pages = {179--183},
	file = {Cappellin et al. - 2011 - Extending the dynamic range of proton transfer rea.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\TLG9HLX3\\Cappellin et al. - 2011 - Extending the dynamic range of proton transfer rea.pdf:application/pdf}
}

@article{cappellin_improved_2010,
	title = {Improved mass accuracy in {PTR}-{TOF}-{MS}: {Another} step towards better compound identification in {PTR}-{MS}},
	volume = {290},
	issn = {13873806},
	shorttitle = {Improved mass accuracy in {PTR}-{TOF}-{MS}},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1387380609003571},
	doi = {10.1016/j.ijms.2009.11.007},
	abstract = {Proton transfer reaction mass spectrometry (PTR-MS) provides on-line monitoring of volatile organic compounds (VOCs) with a low detection threshold and a fast response time. Commercially available set-ups are usually based on quadrupole analysers that, due to the unit mass resolution, do not provide useful analytical information besides the nominal mass of the ions detected. Recently new instruments based on time-of-ﬂight (PTR-TOF-MS) analysers have been proposed and commercialized. They provide higher mass resolution and thus improve the analytical information contained in the spectra. Mass accuracy, however, is an issue that has not been considered in great detail in the published papers on PTR-TOF-MS so far. We show here that the mass accuracy obtained by a commercial apparatus can be improved by proper data analysis. In particular, internal calibration based on an improved algorithm allows for a mass accuracy that sufﬁces for elemental determination in the most common situations. Achieving good mass accuracy is a fundamental step for further exploiting the analytical potential of PTR-MS.},
	language = {en},
	number = {1},
	urldate = {2019-01-31},
	journal = {International Journal of Mass Spectrometry},
	author = {Cappellin, Luca and Biasioli, Franco and Fabris, Alessandra and Schuhfried, Erna and Soukoulis, Christos and Märk, Tilmann D. and Gasperi, Flavia},
	month = feb,
	year = {2010},
	pages = {60--63},
	file = {Cappellin et al. - 2010 - Improved mass accuracy in PTR-TOF-MS Another step.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\H9M9JVFV\\Cappellin et al. - 2010 - Improved mass accuracy in PTR-TOF-MS Another step.pdf:application/pdf}
}

@article{cappellin_data_2011,
	title = {On data analysis in {PTR}-{TOF}-{MS}: {From} raw spectra to data mining},
	volume = {155},
	issn = {09254005},
	shorttitle = {On data analysis in {PTR}-{TOF}-{MS}},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0925400510009135},
	doi = {10.1016/j.snb.2010.11.044},
	abstract = {Recently the coupling of proton transfer reaction ionization with a time-of-ﬂight mass analyser (PTRTOF-MS) has been proposed to realise a volatile organic compound (VOC) detector that overcomes the limitations in terms of time and mass resolution of the previous instrument based on a quadrupole mass analysers (PTR-Quad-MS). This opens new horizons for research and allows for new applications in ﬁelds where the rapid and sensitive monitoring and quantiﬁcation of volatile organic compounds (VOCs) is crucial as, for instance, environmental sciences, food sciences and medicine. In particular, if coupled with appropriate data mining methods, it can provide a fast MS-nose system with rich analytical information. The main, perhaps even the only, drawback of this new technique in comparison to its precursor is related to the increased size and complexity of the data sets obtained. It appears that this is the main limitation to its full use and widespread application. Here we present and discuss a complete computer-based strategy for the data analysis of PTR-TOF-MS data from basic mass spectra handling, to the application of up-to date data mining methods. As a case study we apply the whole procedure to the classiﬁcation of apple cultivars and clones, which was based on the distinctive proﬁles of volatile organic compound emissions.},
	language = {en},
	number = {1},
	urldate = {2019-01-31},
	journal = {Sensors and Actuators B: Chemical},
	author = {Cappellin, Luca and Biasioli, Franco and Granitto, Pablo M. and Schuhfried, Erna and Soukoulis, Christos and Costa, Fabrizio and Märk, Tilmann D. and Gasperi, Flavia},
	month = jul,
	year = {2011},
	pages = {183--190},
	file = {Cappellin et al. - 2011 - On data analysis in PTR-TOF-MS From raw spectra t.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\DGAHAJEW\\Cappellin et al. - 2011 - On data analysis in PTR-TOF-MS From raw spectra t.pdf:application/pdf}
}

@article{cappellin_ptr-tof-ms_2012,
	title = {{PTR}-{ToF}-{MS} and data mining methods: a new tool for fruit metabolomics},
	volume = {8},
	issn = {1573-3882, 1573-3890},
	shorttitle = {{PTR}-{ToF}-{MS} and data mining methods},
	url = {http://link.springer.com/10.1007/s11306-012-0405-9},
	doi = {10.1007/s11306-012-0405-9},
	language = {en},
	number = {5},
	urldate = {2019-01-31},
	journal = {Metabolomics},
	author = {Cappellin, Luca and Soukoulis, Christos and Aprea, Eugenio and Granitto, Pablo and Dallabetta, Nicola and Costa, Fabrizio and Viola, Roberto and Märk, Tilmann D. and Gasperi, Flavia and Biasioli, Franco},
	month = oct,
	year = {2012},
	pages = {761--770},
	file = {Cappellin et al. - 2012 - PTR-ToF-MS and data mining methods a new tool for.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\57NP7HKV\\Cappellin et al. - 2012 - PTR-ToF-MS and data mining methods a new tool for.pdf:application/pdf}
}

@article{graus_high_2010,
	title = {High resolution {PTR}-{TOF}: {Quantification} and formula confirmation of {VOC} in real time},
	volume = {21},
	issn = {1044-0305, 1879-1123},
	shorttitle = {High resolution {PTR}-{TOF}},
	url = {http://link.springer.com/10.1016/j.jasms.2010.02.006},
	doi = {10.1016/j.jasms.2010.02.006},
	language = {en},
	number = {6},
	urldate = {2019-01-31},
	journal = {Journal of the American Society for Mass Spectrometry},
	author = {Graus, Martin and Müller, Markus and Hansel, Armin},
	month = jun,
	year = {2010},
	pages = {1037--1044},
	file = {Graus et al. - 2010 - High resolution PTR-TOF Quantification and formul.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\VJ3FTLFU\\Graus et al. - 2010 - High resolution PTR-TOF Quantification and formul.pdf:application/pdf}
}

@article{titzmann_improved_2010,
	title = {Improved peak analysis of signals based on counting systems: {Illustrated} for proton-transfer-reaction time-of-flight mass spectrometry},
	volume = {295},
	issn = {13873806},
	shorttitle = {Improved peak analysis of signals based on counting systems},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1387380610002459},
	doi = {10.1016/j.ijms.2010.07.009},
	abstract = {Statistical analysis of measured signals from counting systems is a common method to increase the accuracy and precision of peak position and peak area. The most common approach to analyze data gained from counting systems is to ﬁt the data peak by peak using an appropriate probability density function (PDF) like a Gaussian function. Since a counting system creates histograms, the counted data do not represent data points of the anticipated PDF. Therefore, one should not ﬁt any PDF directly to the histogram data. Here we present a solution to this problem by ﬁtting distributions instead of densities. A simple formula allows to correct for Poisson statistics and dead-time effects. The improved peak analysis method is applied to mass spectra obtained from a recently developed proton-transfer-reaction time-ofﬂight mass spectrometer (PTR-TOF) enhancing the mass accuracy and peak quantiﬁcation.},
	language = {en},
	number = {1-2},
	urldate = {2019-01-31},
	journal = {International Journal of Mass Spectrometry},
	author = {Titzmann, Thorsten and Graus, Martin and Müller, Markus and Hansel, Armin and Ostermann, Alexander},
	month = jul,
	year = {2010},
	pages = {72--77},
	file = {Titzmann et al. - 2010 - Improved peak analysis of signals based on countin.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\WFQ6E2DM\\Titzmann et al. - 2010 - Improved peak analysis of signals based on countin.pdf:application/pdf}
}

@article{muller_enhanced_2011,
	title = {Enhanced spectral analysis of {C}-{TOF} {Aerosol} {Mass} {Spectrometer} data: {Iterative} residual analysis and cumulative peak fitting},
	volume = {306},
	issn = {13873806},
	shorttitle = {Enhanced spectral analysis of {C}-{TOF} {Aerosol} {Mass} {Spectrometer} data},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1387380611001576},
	doi = {10.1016/j.ijms.2011.04.007},
	abstract = {We present a method for an improved spectral analysis of datasets measured by a C-TOF Aerosol Mass Spectrometer. Using cumulative peak ﬁtting and iterative residual analysis, multiple isobaric peaks can be separated. These algorithms are described and are tested in various simulations, which have been performed to determine the beneﬁts and constraints of this method. A smog chamber example is presented to demonstrate the performance and constraints for real data, with an example focusing on m/z 43. In this case, two isobaric peaks can be separated (m/z 43.015 and m/z 43.043) and identiﬁed as C2H3O+ and C2H5N+ respectively. Indistinguishable isobaric interferences slightly shift the exact m/z ratios resulting in a worse mass accuracy as expected from the simulations. Nevertheless, a 50 ppm mass accuracy is achieved, which is an impressive value for the identiﬁcation of two isobaric peaks separated by 0.65 full width half maximum for an instrument with a mass resolving power of only R = 1000. According to the simulations, a mass resolving power of at least 4000 would be necessary to quantitatively separate the expected isobaric interferences that are separated by a m/z difference of about 0.004 at m/z 43.},
	language = {en},
	number = {1},
	urldate = {2019-01-31},
	journal = {International Journal of Mass Spectrometry},
	author = {Müller, Markus and George, Christian and D’Anna, Barbara},
	month = sep,
	year = {2011},
	pages = {1--8},
	file = {Müller et al. - 2011 - Enhanced spectral analysis of C-TOF Aerosol Mass S.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\8KXYN7YZ\\Müller et al. - 2011 - Enhanced spectral analysis of C-TOF Aerosol Mass S.pdf:application/pdf}
}

@article{muller_new_2013,
	title = {A new software tool for the analysis of high resolution {PTR}-{TOF} mass spectra},
	volume = {127},
	issn = {01697439},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0169743913001275},
	doi = {10.1016/j.chemolab.2013.06.011},
	abstract = {The High Resolution Proton-Transfer-Reaction Time-of-Flight Mass Spectrometer (HR PTR-TOF-MS) is a powerful analytical tool used by various scientiﬁc communities for real-time measurements of volatile organic compounds (VOC). The analysis of HR PTR-TOF-MS data is, however, particularly demanding because of the large amount of complex data being generated. Based on recently developed or described mathematical methods, we have produced a new software tool, the PTR-TOF Data Analyzer, which greatly facilitates the data analysis process. The new software solution allows for i) a combined Poisson counting statistics and dead time correction of ion count rates, ii) accurate mass axis calibration, iii) an iterative residual peak analysis that detects up to 5 isobaric peaks per unit m/z, iv) time series analysis of both low and high mass and time resolution data and v) visualization of analysis results for fast quality assurance checks. After having been successfully tested by a group of users with different application needs, the PTR-TOF Data Analyzer is made generally available to the scientiﬁc community. This will improve the user-friendliness of the PTR-TOF-MS technique and facilitate scientiﬁc work with this new analytical mass spectrometer.},
	language = {en},
	urldate = {2019-01-31},
	journal = {Chemometrics and Intelligent Laboratory Systems},
	author = {Müller, Markus and Mikoviny, Tomáš and Jud, Werner and D'Anna, Barbara and Wisthaler, Armin},
	month = aug,
	year = {2013},
	pages = {158--165},
	file = {Müller et al. - 2013 - A new software tool for the analysis of high resol.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\HZ4599R8\\Müller et al. - 2013 - A new software tool for the analysis of high resol.pdf:application/pdf}
}

@article{muller_detector_2014,
	title = {Detector aging induced mass discrimination and non-linearity effects in {PTR}-{ToF}-{MS}},
	volume = {365-366},
	issn = {13873806},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1387380613004338},
	doi = {10.1016/j.ijms.2013.12.008},
	abstract = {In this short technical paper we demonstrate how aging of the micro-channel plate (MCP) detector in a PTR-ToF-MS instrument induces strong mass discrimination and detection non-linearity effects. Based on exemplary data from an 11-week measurement campaign we show how detector aging led to an m/zdependent loss in detection efﬁciency in the m/z 33 (−19\%) to m/z 205 range (−67\%). Ion signals in the upper m/z range did not increase linearly with analyte concentration (0–150 ppbv) when the MCP detector was not operated in the saturation regime. Both effects may lead to large errors in VOC quantiﬁcation by PTR-ToF-MS if the instrument is not externally calibrated on a frequent basis. We also demonstrate that the current practice of minimizing ion feedback in the MCP detector will trigger the described problems. Our study may serve as a guide for diagnosing and optimizing PTR-ToF-MS detector performance.},
	language = {en},
	urldate = {2019-01-31},
	journal = {International Journal of Mass Spectrometry},
	author = {Müller, M. and Mikoviny, T. and Wisthaler, A.},
	month = may,
	year = {2014},
	pages = {93--97},
	file = {Müller et al. - 2014 - Detector aging induced mass discrimination and non.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\YKJDF6A6\\Müller et al. - 2014 - Detector aging induced mass discrimination and non.pdf:application/pdf}
}

@article{herbig_-line_2009,
	title = {On-line breath analysis with {PTR}-{TOF}},
	volume = {3},
	issn = {1752-7155, 1752-7163},
	url = {http://stacks.iop.org/1752-7163/3/i=2/a=027004?key=crossref.cd366040f247a8c9557af6c2233e90f2},
	doi = {10.1088/1752-7155/3/2/027004},
	abstract = {We report on on-line breath gas analysis with a new type of analytical instrument, which represents the next generation of proton-transfer-reaction mass spectrometers. This time-of-ﬂight mass spectrometer in combination with the soft proton-transfer-reaction ionization (PTR-TOF) offers numerous advantages for the sensitive detection of volatile organic compounds and overcomes several limitations. First, a time-of-ﬂight instrument allows for a measurement of a complete mass spectrum within a fraction of a second. Second, a high mass resolving power enables the separation of isobaric molecules and the identiﬁcation of their chemical composition. We present the ﬁrst on-line breath measurements with a PTR-TOF and demonstrate the advantages for on-line breath analysis. In combination with buffered end-tidal (BET) sampling, we obtain a complete mass spectrum up to 320 Th within one exhalation with a signal-to-noise ratio sufﬁcient to measure down to pptv levels. We exploit the high mass resolving power to identify the main components in the breath composition of several healthy volunteers.},
	language = {en},
	number = {2},
	urldate = {2019-01-31},
	journal = {Journal of Breath Research},
	author = {Herbig, Jens and Müller, Markus and Schallhart, Simon and Titzmann, Thorsten and Graus, Martin and Hansel, Armin},
	month = jun,
	year = {2009},
	pages = {027004},
	file = {Herbig et al. - 2009 - On-line breath analysis with PTR-TOF.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\K375S4GA\\Herbig et al. - 2009 - On-line breath analysis with PTR-TOF.pdf:application/pdf}
}

@article{picaud_linear_2018,
	title = {Linear {MALDI}-{ToF} simultaneous spectrum deconvolution and baseline removal},
	volume = {19},
	issn = {1471-2105},
	url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2116-3},
	doi = {10.1186/s12859-018-2116-3},
	abstract = {Background: Thanks to a reasonable cost and simple sample preparation procedure, linear MALDI-ToF spectrometry is a growing technology for clinical microbiology. With appropriate spectrum databases, this technology can be used for early identification of pathogens in body fluids. However, due to the low resolution of linear MALDI-ToF instruments, robust and accurate peak picking remains a challenging task. In this context we propose a new peak extraction algorithm from raw spectrum. With this method the spectrum baseline and spectrum peaks are processed jointly. The approach relies on an additive model constituted by a smooth baseline part plus a sparse peak list convolved with a known peak shape. The model is then fitted under a Gaussian noise model. The proposed method is well suited to process low resolution spectra with important baseline and unresolved peaks.
Results: We developed a new peak deconvolution procedure. The paper describes the method derivation and discusses some of its interpretations. The algorithm is then described in a pseudo-code form where the required optimization procedure is detailed. For synthetic data the method is compared to a more conventional approach. The new method reduces artifacts caused by the usual two-steps procedure, baseline removal then peak extraction. Finally some results on real linear MALDI-ToF spectra are provided.
Conclusions: We introduced a new method for peak picking, where peak deconvolution and baseline computation are performed jointly. On simulated data we showed that this global approach performs better than a classical one where baseline and peaks are processed sequentially. A dedicated experiment has been conducted on real spectra. In this study a collection of spectra of spiked proteins were acquired and then analyzed. Better performances of the proposed method, in term of accuracy and reproductibility, have been observed and validated by an extended statistical analysis.},
	language = {en},
	number = {1},
	urldate = {2019-01-31},
	journal = {BMC Bioinformatics},
	author = {Picaud, Vincent and Giovannelli, Jean-Francois and Truntzer, Caroline and Charrier, Jean-Philippe and Giremus, Audrey and Grangeat, Pierre and Mercier, Catherine},
	month = dec,
	year = {2018},
	file = {Picaud et al. - 2018 - Linear MALDI-ToF simultaneous spectrum deconvoluti.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\BI9J9C6W\\Picaud et al. - 2018 - Linear MALDI-ToF simultaneous spectrum deconvoluti.pdf:application/pdf}
}

@article{rattray_taking_2014,
	title = {Taking your breath away: metabolomics breathes life in to personalized medicine},
	volume = {32},
	issn = {01677799},
	shorttitle = {Taking your breath away},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0167779914001632},
	doi = {10.1016/j.tibtech.2014.08.003},
	language = {en},
	number = {10},
	urldate = {2019-01-31},
	journal = {Trends in Biotechnology},
	author = {Rattray, Nicholas J.W. and Hamrang, Zahra and Trivedi, Drupad K. and Goodacre, Royston and Fowler, Stephen J.},
	month = oct,
	year = {2014},
	pages = {538--548},
	file = {Rattray et al. - 2014 - Taking your breath away metabolomics breathes lif.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\59HX43MD\\Rattray et al. - 2014 - Taking your breath away metabolomics breathes lif.pdf:application/pdf}
}

@article{hansel_proton_1995,
	title = {Proton transfer reaction mass spectrometry: on-line trace gas analysis at the ppb level},
	volume = {149-150},
	issn = {01681176},
	shorttitle = {Proton transfer reaction mass spectrometry},
	url = {http://linkinghub.elsevier.com/retrieve/pii/016811769504294U},
	doi = {10.1016/0168-1176(95)04294-U},
	abstract = {A system for trace gas analysis using proton transfer reaction mass spectrometry (PTR-MS) has been developed which allows for on-line measurements of components with concentrations as low as 1 ppb. The method is based on reactions of HsO+ ions, which perform non-dissociative proton transfer to most of the common organic trace constituents but do not react with any of the components present in clean air. Examples of analysis of breath taken from smokers and non-smokers as well as from patients suffering from cirrhosis of the liver, and of air in buildings as well as of ambient air taken at a road crossing demonstrate the wide range of applicability of this method. An enhanced level of acetonitrile in the breath is a most suitable indicator that a person is a smoker. Enhanced levels of propanol strongly indicate that a person has a severe liver deficiency.},
	language = {en},
	urldate = {2019-01-31},
	journal = {International Journal of Mass Spectrometry and Ion Processes},
	author = {Hansel, A. and Jordan, A. and Holzinger, R. and Prazeller, P. and Vogel, W. and Lindinger, W.},
	month = nov,
	year = {1995},
	pages = {609--619},
	file = {Hansel et al. - 1995 - Proton transfer reaction mass spectrometry on-lin.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\BT5GEE4I\\Hansel et al. - 1995 - Proton transfer reaction mass spectrometry on-lin.pdf:application/pdf}
}

@article{titzmann_improved_2010-1,
	title = {Improved peak analysis of signals based on counting systems: {Illustrated} for proton-transfer-reaction time-of-flight mass spectrometry},
	volume = {295},
	issn = {13873806},
	shorttitle = {Improved peak analysis of signals based on counting systems},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1387380610002459},
	doi = {10.1016/j.ijms.2010.07.009},
	abstract = {Statistical analysis of measured signals from counting systems is a common method to increase the accuracy and precision of peak position and peak area. The most common approach to analyze data gained from counting systems is to ﬁt the data peak by peak using an appropriate probability density function (PDF) like a Gaussian function. Since a counting system creates histograms, the counted data do not represent data points of the anticipated PDF. Therefore, one should not ﬁt any PDF directly to the histogram data. Here we present a solution to this problem by ﬁtting distributions instead of densities. A simple formula allows to correct for Poisson statistics and dead-time effects. The improved peak analysis method is applied to mass spectra obtained from a recently developed proton-transfer-reaction time-ofﬂight mass spectrometer (PTR-TOF) enhancing the mass accuracy and peak quantiﬁcation.},
	language = {en},
	number = {1-2},
	urldate = {2019-02-18},
	journal = {International Journal of Mass Spectrometry},
	author = {Titzmann, Thorsten and Graus, Martin and Müller, Markus and Hansel, Armin and Ostermann, Alexander},
	month = jul,
	year = {2010},
	pages = {72--77},
	file = {Titzmann et al. - 2010 - Improved peak analysis of signals based on countin.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\G3NBUIHS\\Titzmann et al. - 2010 - Improved peak analysis of signals based on countin.pdf:application/pdf}
}

@article{clayton_snip_nodate,
	title = {{SNIP}, {A} {STATISTICS}-{SENSITIVE} {BACKGROUND} {TREATMENT} {FOR} {THE} {QUANTITATIVE} {ANALYSIS} {OF} {PIXE} {SPECTFtA} {IN} {GEOSCIENCE} {APPLICATIONS}},
	language = {en},
	author = {CLAYTON, C G RYAN and Clayton, E and Griffin, W L and Sie, S H},
	pages = {7},
	file = {If et al. - SNIP, A STATISTICS-SENSITIVE BACKGROUND TREATMENT .pdf:C\:\\Users\\CR258086\\Zotero\\storage\\GJHWT444\\If et al. - SNIP, A STATISTICS-SENSITIVE BACKGROUND TREATMENT .pdf:application/pdf}
}

@article{jordan_high_2009,
	title = {A high resolution and high sensitivity proton-transfer-reaction time-of-flight mass spectrometer ({PTR}-{TOF}-{MS})},
	volume = {286},
	issn = {13873806},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1387380609002371},
	doi = {10.1016/j.ijms.2009.07.005},
	abstract = {Proton-transfer-reaction mass spectrometry (PTR-MS) developed about 10 years ago is used today in a wide range of scientiﬁc and technical ﬁelds allowing real-time on-line measurements of volatile organic compounds in air with a high sensitivity and a fast response time. Most instruments employed so far use quadrupole ﬁlters to analyze product ions generated in the reaction drift tube. Due to the low mass resolution of the quadrupoles used this has the disadvantage that identiﬁcation of trace gases under study is not unambiguous.},
	language = {en},
	number = {2-3},
	urldate = {2019-02-21},
	journal = {International Journal of Mass Spectrometry},
	author = {Jordan, A. and Haidacher, S. and Hanel, G. and Hartungen, E. and Märk, L. and Seehauser, H. and Schottkowsky, R. and Sulzer, P. and Märk, T.D.},
	month = sep,
	year = {2009},
	pages = {122--128},
	file = {Jordan et al. - 2009 - A high resolution and high sensitivity proton-tran.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\YXW2TM6F\\Jordan et al. - 2009 - A high resolution and high sensitivity proton-tran.pdf:application/pdf}
}

@article{savitzky_smoothing_1964,
	title = {Smoothing and {Differentiation} of {Data} by {Simplified} {Least} {Squares} {Procedures}.},
	volume = {36},
	issn = {0003-2700, 1520-6882},
	url = {http://pubs.acs.org/doi/abs/10.1021/ac60214a047},
	doi = {10.1021/ac60214a047},
	language = {en},
	number = {8},
	urldate = {2019-03-05},
	journal = {Analytical Chemistry},
	author = {Savitzky, Abraham. and Golay, M. J. E.},
	month = jul,
	year = {1964},
	pages = {1627--1639},
	file = {Savitzky et Golay - 1964 - Smoothing and Differentiation of Data by Simplifie.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\X7SU4L6G\\Savitzky et Golay - 1964 - Smoothing and Differentiation of Data by Simplifie.pdf:application/pdf}
}

@article{vivo-truyols_automatic_2006,
	title = {Automatic {Selection} of {Optimal} {Savitzky}−{Golay} {Smoothing}},
	volume = {78},
	issn = {0003-2700, 1520-6882},
	url = {https://pubs.acs.org/doi/10.1021/ac0600196},
	doi = {10.1021/ac0600196},
	language = {en},
	number = {13},
	urldate = {2019-03-06},
	journal = {Analytical Chemistry},
	author = {Vivó-Truyols, Gabriel and Schoenmakers, Peter J.},
	month = jul,
	year = {2006},
	pages = {4598--4608},
	file = {Vivó-Truyols et Schoenmakers - 2006 - Automatic Selection of Optimal Savitzky−Golay Smoo.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\TAC8D96D\\Vivó-Truyols et Schoenmakers - 2006 - Automatic Selection of Optimal Savitzky−Golay Smoo.pdf:application/pdf}
}

@article{herbig_buffered_2008,
	title = {Buffered end-tidal ({BET}) sampling—a novel method for real-time breath-gas analysis},
	volume = {2},
	issn = {1752-7155, 1752-7163},
	url = {http://stacks.iop.org/1752-7163/2/i=3/a=037008?key=crossref.6c1463e66d0714dce9de2a6cfe05bf66},
	doi = {10.1088/1752-7155/2/3/037008},
	abstract = {We present a novel method for real-time breath-gas analysis using mass-spectrometric techniques: buffered end-tidal (BET) on-line sampling. BET has several advantages over conventional direct on-line sampling where the subject inhales and exhales through a sampling tube. In our approach, a single exhalation is administered through a tailored tube in which the end-tidal fraction of the breath-gas sample is buffered. This increases sampling time by an order of magnitude to several seconds, improving signal quality and reducing the total measurement time per test subject. Furthermore, only one exhalation per minute is required for sampling and the test subject can otherwise maintain a normal breathing pattern, thereby reducing the risk of hyperventilation. To validate our new BET sampling method we conducted comparative measurements with direct on-line sampling using proton-transfer-reaction mass spectrometry. We ﬁnd excellent agreement in measured acetone and acetonitrile concentrations. High variability observed in breath-by-breath isoprene concentrations is attributed to differences in exhalation depth and inﬂuences of hyperventilation on end-tidal concentrations.},
	language = {en},
	number = {3},
	urldate = {2019-03-11},
	journal = {Journal of Breath Research},
	author = {Herbig, Jens and Titzmann, Thorsten and Beauchamp, Jonathan and Kohl, Ingrid and Hansel, Armin},
	month = sep,
	year = {2008},
	pages = {037008},
	file = {Herbig et al. - 2008 - Buffered end-tidal (BET) sampling—a novel method f.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\7TW4ILFY\\Herbig et al. - 2008 - Buffered end-tidal (BET) sampling—a novel method f.pdf:application/pdf}
}

@article{coles_resolution_1994,
	title = {Resolution limitations from detector pulse width and jitter in a linear orthogonal-acceleration time-of-flight mass spectrometer},
	volume = {5},
	issn = {1044-0305, 1879-1123},
	url = {http://link.springer.com/10.1016/1044-0305(94)80010-3},
	doi = {10.1016/1044-0305(94)80010-3},
	language = {en},
	number = {8},
	urldate = {2019-03-12},
	journal = {Journal of the American Society for Mass Spectrometry},
	author = {Coles, J. N. and Guilhaus, M.},
	month = aug,
	year = {1994},
	pages = {772--778},
	file = {Coles et Guilhaus - 1994 - Resolution limitations from detector pulse width a.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\BXGETR9P\\Coles et Guilhaus - 1994 - Resolution limitations from detector pulse width a.pdf:application/pdf}
}

@article{yang_comparison_2009,
	title = {Comparison of public peak detection algorithms for {MALDI} mass spectrometry data analysis},
	volume = {10},
	issn = {1471-2105},
	url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-4},
	doi = {10.1186/1471-2105-10-4},
	abstract = {Background: In mass spectrometry (MS) based proteomic data analysis, peak detection is an essential step for subsequent analysis. Recently, there has been significant progress in the development of various peak detection algorithms. However, neither a comprehensive survey nor an experimental comparison of these algorithms is yet available. The main objective of this paper is to provide such a survey and to compare the performance of single spectrum based peak detection methods.
Results: In general, we can decompose a peak detection procedure into three consequent parts: smoothing, baseline correction and peak finding. We first categorize existing peak detection algorithms according to the techniques used in different phases. Such a categorization reveals the differences and similarities among existing peak detection algorithms. Then, we choose five typical peak detection algorithms to conduct a comprehensive experimental study using both simulation data and real MALDI MS data.
Conclusion: The results of comparison show that the continuous wavelet-based algorithm provides the best average performance.},
	language = {en},
	number = {1},
	urldate = {2019-03-20},
	journal = {BMC Bioinformatics},
	author = {Yang, Chao and He, Zengyou and Yu, Weichuan},
	month = dec,
	year = {2009},
	file = {Yang et al. - 2009 - Comparison of public peak detection algorithms for.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\5FY82BPN\\Yang et al. - 2009 - Comparison of public peak detection algorithms for.pdf:application/pdf}
}

@article{ruckstuhl_baseline_2001,
	title = {Baseline subtraction using robust local regression estimation},
	volume = {68},
	issn = {00224073},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0022407300000212},
	doi = {10.1016/S0022-4073(00)00021-2},
	abstract = {A technique entitled robust baseline estimation is introduced, which uses techniques of robust local regression to estimate baselines in spectra that consist of sharp features superimposed upon a continuous, slowly varying baseline. The technique is applied to synthetic spectra, to evaluate its capabilities, and to laser-induced \#uorescence spectra of OH (produced from the reaction of ozone with hydrogen atoms). The latter example is a particularly challenging case for baseline estimation because the experimental noise varies as a function of frequency. 2000 Elsevier Science Ltd. All rights reserved.},
	language = {en},
	number = {2},
	urldate = {2019-03-20},
	journal = {Journal of Quantitative Spectroscopy and Radiative Transfer},
	author = {Ruckstuhl, Andreas F. and Jacobson, Matthew P. and Field, Robert W. and Dodd, James A.},
	month = jan,
	year = {2001},
	pages = {179--193},
	file = {Ruckstuhl et al. - 2001 - Baseline subtraction using robust local regression.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\VJGE8JFZ\\Ruckstuhl et al. - 2001 - Baseline subtraction using robust local regression.pdf:application/pdf}
}

@article{gan_baseline_2006,
	title = {Baseline correction by improved iterative polynomial fitting with automatic threshold},
	volume = {82},
	issn = {01697439},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0169743905001589},
	doi = {10.1016/j.chemolab.2005.08.009},
	abstract = {An iterative polynomial fitting method is proposed for the estimate of the baseline of chemical signal. The new method generates automatic thresholds by comparing the chemical signal with the calculated signal from polynomial fitting in the iterative processes. The signal peaks are cut out consecutively in the iterative processes so the polynomial fitting will finally give a good estimation of the baseline. Simulated data and real data from capillary electrophoresis experiment are used to demonstrate the feasibility of the proposed method.},
	language = {en},
	number = {1-2},
	urldate = {2019-03-20},
	journal = {Chemometrics and Intelligent Laboratory Systems},
	author = {Gan, Feng and Ruan, Guihua and Mo, Jinyuan},
	month = may,
	year = {2006},
	pages = {59--65},
	file = {Gan et al. - 2006 - Baseline correction by improved iterative polynomi.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\BSDL2P46\\Gan et al. - 2006 - Baseline correction by improved iterative polynomi.pdf:application/pdf}
}

@article{mazet_background_2005,
	title = {Background removal from spectra by designing and minimising a non-quadratic cost function},
	volume = {76},
	issn = {01697439},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0169743904002412},
	doi = {10.1016/j.chemolab.2004.10.003},
	abstract = {In this paper, the problem of estimating the background of a spectrum is addressed. We propose to fit this background to a low-order polynomial, but rather than determining the polynomial parameters that minimise a least-squares criterion (i.e. a quadratic cost function), non-quadratic cost functions well adapted to the problem are proposed. To minimise these cost functions, we use the half-quadratic minimisation. It yields a fast and simple method, which can be applied to a wide range of spectroscopic signal. Guidelines for the choice of the design parameters are given and illustrated on simulated spectra. Finally, the effectiveness of the method is shown by processing experimental infrared and Raman spectra.},
	language = {en},
	number = {2},
	urldate = {2019-03-20},
	journal = {Chemometrics and Intelligent Laboratory Systems},
	author = {Mazet, Vincent and Carteret, Cédric and Brie, David and Idier, Jérôme and Humbert, Bernard},
	month = apr,
	year = {2005},
	pages = {121--133},
	file = {Mazet et al. - 2005 - Background removal from spectra by designing and m.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\SKHFNIUQ\\Mazet et al. - 2005 - Background removal from spectra by designing and m.pdf:application/pdf}
}

@article{pereira_breath_2015,
	title = {Breath {Analysis} as a {Potential} and {Non}-{Invasive} {Frontier} in {Disease} {Diagnosis}: {An} {Overview}},
	volume = {5},
	issn = {2218-1989},
	shorttitle = {Breath {Analysis} as a {Potential} and {Non}-{Invasive} {Frontier} in {Disease} {Diagnosis}},
	url = {http://www.mdpi.com/2218-1989/5/1/3},
	doi = {10.3390/metabo5010003},
	language = {en},
	number = {1},
	urldate = {2019-03-22},
	journal = {Metabolites},
	author = {Pereira, Jorge and Porto-Figueira, Priscilla and Cavaco, Carina and Taunk, Khushman and Rapole, Srikanth and Dhakne, Rahul and Nagarajaram, Hampapathalu and Câmara, José},
	month = jan,
	year = {2015},
	pages = {3--55},
	file = {Pereira et al. - 2015 - Breath Analysis as a Potential and Non-Invasive Fr.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\JAIGJ5HS\\Pereira et al. - 2015 - Breath Analysis as a Potential and Non-Invasive Fr.pdf:application/pdf}
}

@article{dolch_quantification_2015,
	title = {Quantification of propionaldehyde in breath of patients after lung transplantation},
	volume = {85},
	issn = {08915849},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0891584915001653},
	doi = {10.1016/j.freeradbiomed.2015.04.003},
	abstract = {Oxygen-derived free radicals (ROS) have been identiﬁed to contribute signiﬁcantly to ischemia–reperfusion (I/R) injury by initiating chain reactions with polyunsaturated membrane lipids (lipid peroxidation, LPO) resulting in the generation of several aldehydes and ketones. Due to their volatile nature these LPO products can be measured noninvasively in breath. We hypothesized that one of these markers, namely propionaldehyde, will be increased in lung and heart–lung transplant patients where severe oxidative stress due to I/R injury with early graft dysfunction represents one of the major postoperative complications resulting in prolonged ventilation and increased in-hospital morbidity and mortality. Expiratory air measurements for acetone, isoprene, and propionaldehyde were performed in seven patients after lung (n ¼5) or heart–lung (n ¼2) transplantation, ventilated patients (n ¼ 12), and healthy volunteers (n ¼17) using online ion-molecule reaction mass spectrometry. Increased concentrations of acetone (transplanted: 3812 [2347–12498]; ventilated: 1255 [276–1959]; healthy: 631 [520–784] ppbv; P o.001) and propionaldehyde (transplanted: 270 [70–424]; ventilated: 82 [41.8–142]; healthy: 1.7 [0.1–11.8] ppbv; P o.001) were found in expiratory air of transplanted and ventilated patients. Propionaldehyde resulting from spontaneous fragmentation of peroxides due to free radical-induced LPO after I/R injury in patients after lung or heart–lung transplantation can be quantiﬁed in expired breath.},
	language = {en},
	urldate = {2019-03-22},
	journal = {Free Radical Biology and Medicine},
	author = {Dolch, M.E. and Choukèr, A. and Hornuss, C. and Frey, L. and Irlbeck, M. and Praun, S. and Leidlmair, C. and Villinger, J. and Schelling, G.},
	month = aug,
	year = {2015},
	pages = {157--164},
	file = {Dolch et al. - 2015 - Quantification of propionaldehyde in breath of pat.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\MQGWQ6F9\\Dolch et al. - 2015 - Quantification of propionaldehyde in breath of pat.pdf:application/pdf}
}

@article{chen_sensitive_2016,
	title = {A {Sensitive} {NanoString}-{Based} {Assay} to {Score} {STK11} ({LKB1}) {Pathway} {Disruption} in {Lung} {Adenocarcinoma}},
	volume = {11},
	issn = {15560864},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1556086416004287},
	doi = {10.1016/j.jtho.2016.02.009},
	abstract = {Introduction: Serine/threonine kinase 11 gene (STK11), better known as liver kinase b1, is a tumor suppressor that is commonly mutated in lung adenocarcinoma (LUAD). Previous work has shown that mutational inactivation of the STK11 pathway may serve as a predictive biomarker for cancer treatments, including phenformin and cyclooxygenase-2 inhibition. Although immunohistochemical (IHC) staining and diagnostic sequencing are used to measure STK11 pathway disruption, there are serious limitations to these methods, thus emphasizing the importance of validating a clinically useful assay.},
	language = {en},
	number = {6},
	urldate = {2019-03-22},
	journal = {Journal of Thoracic Oncology},
	author = {Chen, Lu and Engel, Brienne E. and Welsh, Eric A. and Yoder, Sean J. and Brantley, Stephen G. and Chen, Dung-Tsa and Beg, Amer A. and Cao, Chunxia and Kaye, Frederic J. and Haura, Eric B. and Schabath, Matthew B. and Cress, W. Douglas},
	month = jun,
	year = {2016},
	pages = {838--849},
	file = {Chen et al. - 2016 - A Sensitive NanoString-Based Assay to Score STK11 .pdf:C\:\\Users\\CR258086\\Zotero\\storage\\NDIEW3IN\\Chen et al. - 2016 - A Sensitive NanoString-Based Assay to Score STK11 .pdf:application/pdf}
}

@article{nardi-agmon_exhaled_2016,
	title = {Exhaled {Breath} {Analysis} for {Monitoring} {Response} to {Treatment} in {Advanced} {Lung} {Cancer}},
	volume = {11},
	issn = {15560864},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1556086416004408},
	doi = {10.1016/j.jtho.2016.02.017},
	abstract = {Introduction: The Response Evaluation Criteria in Solid Tumors (RECIST) serve as the accepted standard to monitor treatment efﬁcacy in lung cancer. However, the time intervals between consecutive computerized tomography scans might be too long to allow early identiﬁcation of treatment failure. This study examines the use of breath sampling to monitor responses to anticancer treatments in patients with advanced lung cancer.
Methods: A total of 143 breath samples were collected from 39 patients with advanced lung cancer. The exhaled breath signature, determined by gas chromatography/mass spectrometry and a nanomaterial-based array of sensors, was correlated with the response to therapy assessed by RECIST: complete response, partial response, stable disease, or progressive disease.
Results: Gas chromatography/mass spectrometry analysis identiﬁed three volatile organic compounds as signiﬁcantly indicating disease control (PR/stable disease), with one of them also signiﬁcantly discriminating PR/stable disease from progressive disease. The nanoarray had the ability to monitor changes in tumor response across therapy, also indicating any lack of further response to therapy. When one-sensor analysis was used, 59\% of the follow-up samples were identiﬁed correctly. There was 85\% success in monitoring disease control (stable disease/partial response).
Conclusion: Breath analysis, using mainly the nanoarray, may serve as a surrogate marker for the response to systemic therapy in lung cancer. As a monitoring tool, it can provide the oncologist with a quick bedside method of identifying a lack of response to an anticancer treatment. This may allow quicker recognition than does the current RECIST analysis. Early recognition of treatment failure},
	language = {en},
	number = {6},
	urldate = {2019-03-22},
	journal = {Journal of Thoracic Oncology},
	author = {Nardi-Agmon, Inbar and Abud-Hawa, Manal and Liran, Ori and Gai-Mor, Naomi and Ilouze, Maya and Onn, Amir and Bar, Jair and Shlomi, Dekel and Haick, Hossam and Peled, Nir},
	month = jun,
	year = {2016},
	pages = {827--837},
	file = {Nardi-Agmon et al. - 2016 - Exhaled Breath Analysis for Monitoring Response to.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\SRQXXVEM\\Nardi-Agmon et al. - 2016 - Exhaled Breath Analysis for Monitoring Response to.pdf:application/pdf}
}

@article{horvath_exhaled_2009,
	title = {Exhaled biomarkers in lung cancer},
	volume = {34},
	issn = {0903-1936, 1399-3003},
	url = {http://erj.ersjournals.com/cgi/doi/10.1183/09031936.00142508},
	doi = {10.1183/09031936.00142508},
	abstract = {Lung cancer is the leading cause of cancer death. Results of therapeutic interventions are particularly discouraging when the disease is discovered in an advanced stage. Early diagnosis is limited by the fact that the disease usually develops asymptomatically and available screening methods do not fulfil the requirements for reliable discrimination between patients with lung cancer and subjects not suffering from the disease. Breath sampling is completely noninvasive and provides a potentially useful approach to screening lung cancer. Exhaled biomarkers contain both volatile and nonvolatile molecules. The profile of volatile organic compounds is different in patients with lung cancer than in control subjects. In exhaled breath condensate, the proteomic profile of breath from cancer patients differs from that of healthy smokers. We reviewed the scientific evidence demonstrating that a unique chemical signature can be detected in the breath of patients with lung cancer and that the exhaled breath biomarker profile could aid clinical decision making.},
	language = {en},
	number = {1},
	urldate = {2019-03-22},
	journal = {European Respiratory Journal},
	author = {Horvath, I. and Lazar, Z. and Gyulai, N. and Kollai, M. and Losonczy, G.},
	month = jul,
	year = {2009},
	pages = {261--275},
	file = {Horvath et al. - 2009 - Exhaled biomarkers in lung cancer.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\PCLJXQZ6\\Horvath et al. - 2009 - Exhaled biomarkers in lung cancer.pdf:application/pdf}
}

@article{phillips_prediction_2007,
	title = {Prediction of lung cancer using volatile biomarkers in breath1},
	volume = {3},
	issn = {18758592, 15740153},
	url = {http://www.medra.org/servlet/aliasResolver?alias=iospress&doi=10.3233/CBM-2007-3204},
	doi = {10.3233/CBM-2007-3204},
	abstract = {Background: Normal metabolism generates several volatile organic compounds (VOCs) that are excreted in the breath (e.g. alkanes). In patients with lung cancer, induction of high-risk cytochrome p450 genotypes may accelerate catabolism of these VOCs, so that their altered abundance in breath may provide biomarkers of lung cancer.},
	language = {en},
	number = {2},
	urldate = {2019-03-22},
	journal = {Cancer Biomarkers},
	author = {Phillips, Michael and Altorki, Nasser and Austin, John H.M. and Cameron, Robert B. and Cataneo, Renee N. and Greenberg, Joel and Kloss, Robert and Maxfield, Roger A. and Munawar, Muhammad I. and Pass, Harvey I. and Rashid, Asif and Rom, William N. and Schmitt, Peter},
	month = apr,
	year = {2007},
	pages = {95--109},
	file = {Phillips et al. - 2007 - Prediction of lung cancer using volatile biomarker.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\G7GY3ZN4\\Phillips et al. - 2007 - Prediction of lung cancer using volatile biomarker.pdf:application/pdf}
}

@article{devillier_metabolomics_2017,
	title = {Metabolomics in the {Diagnosis} and {Pharmacotherapy} of {Lung} {Diseases}},
	volume = {23},
	issn = {13816128},
	url = {http://www.eurekaselect.com/149636/article},
	doi = {10.2174/1381612823666170130155627},
	abstract = {Metabolomics is of the increasing interests in medical research and the study of respiratory diseases. This novel type of small molecule analysis can be performed not only on conventional biological samples such as plasma or urine but also on sputum, bronchoalveolar fluid, exhaled breath condensate or exhaled breath itself (which is particularly relevant for research on respiratory diseases). On one hand, powerful analytical methodologies (including mass spectrometry and nuclear magnetic resonance spectroscopy) are labour-intensive but enable the exhaustive identification of metabolites. On the other hand, electronic noses can be used for exhaled breath analysis. Although the latter devices do not contain metabolite-specific sensors, they produce a condition- or treatment-specific “breathprint” based on pattern recognition. Breath analysis with electronic noses is noninvasive, and can be performed at the bedside in real time. Here, we review the literature on metabolomics studies in respiratory medicine, with a focus on the evaluation of responses to pharmacotherapy.},
	language = {en},
	number = {14},
	urldate = {2019-03-22},
	journal = {Current Pharmaceutical Design},
	author = {Devillier, Philippe and Salvator, Helene and Naline, Emmanuel and Couderc, Louis-Jean and Grassin-Delyle, Stanislas},
	month = may,
	year = {2017},
	file = {Devillier et al. - 2017 - Metabolomics in the Diagnosis and Pharmacotherapy .pdf:C\:\\Users\\CR258086\\Zotero\\storage\\9NGKZIYR\\Devillier et al. - 2017 - Metabolomics in the Diagnosis and Pharmacotherapy .pdf:application/pdf}
}

@article{phillips_variation_1999,
	title = {Variation in volatile organic compounds in the breath of normal humans},
	volume = {729},
	issn = {03784347},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0378434799001279},
	doi = {10.1016/S0378-4347(99)00127-9},
	abstract = {We studied the variation in volatile organic compounds (VOCs) in the breath of 50 normal humans, using gas chromatography and mass spectroscopy. An average breath sample contained 204.2 VOCs (SD519.8, range 157–241).The alveolar gradient of each VOC (abundance in breath minus abundance in air) varied with rate of synthesis minus rate of clearance. A total of 3481 different VOCs were observed: 1753 with positive alveolar gradients, 1728 with negative alveolar gradients. Twenty-seven VOCs were observed in all ﬁfty subjects. This study conﬁrmed previous reports of wide inter-individual variations. Two new ﬁndings were the comparatively small variation in total number of breath VOCs, and the presence of a ‘common core’ of breath VOCs in all subjects. © 1999 Elsevier Science B.V. All rights reserved.},
	language = {en},
	number = {1-2},
	urldate = {2019-03-22},
	journal = {Journal of Chromatography B: Biomedical Sciences and Applications},
	author = {Phillips, Michael and Herrera, Jolanta and Krishnan, Sunithi and Zain, Mooena and Greenberg, Joel and Cataneo, Renee N.},
	month = jun,
	year = {1999},
	pages = {75--88},
	file = {Phillips et al. - 1999 - Variation in volatile organic compounds in the bre.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\VYJQJKCR\\Phillips et al. - 1999 - Variation in volatile organic compounds in the bre.pdf:application/pdf}
}

@article{miekisch_diagnostic_2004,
	title = {Diagnostic potential of breath analysis—focus on volatile organic compounds},
	volume = {347},
	issn = {00098981},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0009898104002256},
	doi = {10.1016/j.cccn.2004.04.023},
	abstract = {Breath analysis has attracted a considerable amount of scientific and clinical interest during the last decade. In contrast to NO, which is predominantly generated in the bronchial system, volatile organic compounds (VOCs) are mainly blood borne and therefore enable monitoring of different processes in the body. Exhaled ethane and pentane concentrations were elevated in inflammatory diseases. Acetone was linked to dextrose metabolism and lipolysis. Exhaled isoprene concentrations showed correlations with cholesterol biosynthesis. Exhaled levels of sulphur-containing compounds were elevated in liver failure and allograft rejection. Looking at a set of volatile markers may enable recognition and diagnosis of complex diseases such as lung or breast cancer. Due to technical problems of sampling and analysis and a lack of normalization and standardization, huge variations exist between results of different studies. This is among the main reasons why breath analysis could not yet been introduced into clinical practice. This review addresses the basic principles of breath analysis and the diagnostic potential of different volatile breath markers. Analytical procedures, issues concerning biochemistry and exhalation mechanisms of volatile substances, and future developments will be discussed.},
	language = {en},
	number = {1-2},
	urldate = {2019-03-22},
	journal = {Clinica Chimica Acta},
	author = {Miekisch, Wolfram and Schubert, Jochen K and Noeldge-Schomburg, Gabriele F.E},
	month = sep,
	year = {2004},
	pages = {25--39},
	file = {Miekisch et al. - 2004 - Diagnostic potential of breath analysis—focus on v.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\45Y38HF3\\Miekisch et al. - 2004 - Diagnostic potential of breath analysis—focus on v.pdf:application/pdf}
}

@book{france_les_2013,
	address = {Paris},
	title = {Les composés organiques volatils: réduction des émissions de {COV} dans l'industrie},
	isbn = {978-2-10-058238-9},
	shorttitle = {Les composés organiques volatils},
	language = {fr},
	publisher = {Dunod},
	author = {{France} and {Agence de l'Environnement et de la Maîtrise de l'Energie}},
	year = {2013},
	note = {OCLC: 829411810},
	file = {VOC.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\H3NIYEPV\\VOC.pdf:application/pdf}
}

@article{de_lacy_costello_review_2014,
	title = {A review of the volatiles from the healthy human body},
	volume = {8},
	issn = {1752-7155, 1752-7163},
	url = {http://stacks.iop.org/1752-7163/8/i=1/a=014001?key=crossref.b6b6a6911efb2c74c533c2e3a6bae189},
	doi = {10.1088/1752-7155/8/1/014001},
	abstract = {A compendium of all the volatile organic compounds (VOCs) emanating from the human body (the volatolome) is for the ﬁrst time reported. 1840 VOCs have been assigned from breath (872), saliva (359), blood (154), milk (256), skin secretions (532) urine (279), and faeces (381) in apparently healthy individuals. Compounds were assigned CAS registry numbers and named according to a common convention where possible. The compounds have been grouped into tables according to their chemical class or functionality to permit easy comparison. Some clear differences are observed, for instance, a lack of esters in urine with a high number in faeces. Careful use of the database is needed. The numbers may not be a true reﬂection of the actual VOCs present from each bodily excretion. The lack of a compound could be due to the techniques used or reﬂect the intensity of effort e.g. there are few publications on VOCs from blood compared to a large number on VOCs in breath. The large number of volatiles reported from skin is partly due to the methodologies used, e.g. collecting excretions on glass beads and then heating to desorb VOCs. All compounds have been included as reported (unless there was a clear discrepancy between name and chemical structure), but there may be some mistaken assignations arising from the original publications, particularly for isomers. It is the authors’ intention that this database will not only be a useful database of VOCs listed in the literature, but will stimulate further study of VOCs from healthy individuals. Establishing a list of volatiles emanating from healthy individuals and increased understanding of VOC metabolic pathways is an important step for differentiating between diseases using VOCs.},
	language = {en},
	number = {1},
	urldate = {2019-05-10},
	journal = {Journal of Breath Research},
	author = {de Lacy Costello, B and Amann, A and Al-Kateb, H and Flynn, C and Filipiak, W and Khalid, T and Osborne, D and Ratcliffe, N M},
	month = jan,
	year = {2014},
	pages = {014001},
	file = {de Lacy Costello et al. - 2014 - A review of the volatiles from the healthy human b.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\CIXD37TV\\de Lacy Costello et al. - 2014 - A review of the volatiles from the healthy human b.pdf:application/pdf}
}

@article{manolls_diagnosticpotentialof_nodate,
	title = {The {DiagnosticPotentialof} {BreathAnalysis}},
	language = {en},
	author = {Manolls, Antony},
	pages = {11},
	file = {Manolls - The DiagnosticPotentialof BreathAnalysis.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\8NCABXT9\\Manolls - The DiagnosticPotentialof BreathAnalysis.pdf:application/pdf}
}

@article{phillips_method_1997,
	title = {Method for the {Collection} and {Assay} of {Volatile} {Organic} {Compounds} in {Breath}},
	volume = {247},
	issn = {00032697},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0003269797920698},
	doi = {10.1006/abio.1997.2069},
	language = {en},
	number = {2},
	urldate = {2019-05-10},
	journal = {Analytical Biochemistry},
	author = {Phillips, Michael},
	month = may,
	year = {1997},
	pages = {272--278},
	file = {Phillips - 1997 - Method for the Collection and Assay of Volatile Or.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\U42LLMHP\\Phillips - 1997 - Method for the Collection and Assay of Volatile Or.pdf:application/pdf}
}

@article{ligor_determination_2009,
	title = {Determination of volatile organic compounds in exhaled breath of patients with lung cancer using solid phase microextraction and gas chromatography mass spectrometry},
	volume = {47},
	issn = {1437-4331, 1434-6621},
	url = {https://www.degruyter.com/view/j/cclm.2009.47.issue-5/cclm.2009.133/cclm.2009.133.xml},
	doi = {10.1515/CCLM.2009.133},
	abstract = {Background: Analysis of exhaled breath is a promising diagnostic method. Sampling of exhaled breath is non-invasive and can be performed as often as considered desirable. There are indications that the concentration and presence of certain of volatile compounds in exhaled breath of lung cancer patients is different from concentrations in healthy volunteers. This might lead to a future diagnostic test for lung cancer.},
	language = {en},
	number = {5},
	urldate = {2019-05-10},
	journal = {Clinical Chemistry and Laboratory Medicine},
	author = {Ligor, Magdalena and Ligor, Tomasz and Bajtarevic, Amel and Ager, Clemens and Pienz, Martin and Klieber, Martin and Denz, Hubert and Fiegl, Michael and Hilbe, Wolfgang and Weiss, Wolfgang and Lukas, Peter and Jamnig, Herbert and Hackl, Martin and Buszewski, Boguslaw and Miekisch, Wolfram and Schubert, Jochen and Amann, Anton},
	month = jan,
	year = {2009},
	file = {Ligor et al. - 2009 - Determination of volatile organic compounds in exh.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\SMYT7TRD\\Ligor et al. - 2009 - Determination of volatile organic compounds in exh.pdf:application/pdf}
}

@article{van_de_kant_clinical_2012,
	title = {Clinical use of exhaled volatile organic compounds in pulmonary diseases: a systematic review},
	volume = {13},
	issn = {1465-9921},
	shorttitle = {Clinical use of exhaled volatile organic compounds in pulmonary diseases},
	url = {http://respiratory-research.com/content/13/1/117},
	doi = {10.1186/1465-9921-13-117},
	abstract = {There is an increasing interest in the potential of exhaled biomarkers, such as volatile organic compounds (VOCs), to improve accurate diagnoses and management decisions in pulmonary diseases. The objective of this manuscript is to systematically review the current knowledge on exhaled VOCs with respect to their potential clinical use in asthma, lung cancer, chronic obstructive pulmonary disease (COPD), cystic fibrosis (CF), and respiratory tract infections. A systematic literature search was performed in PubMed, EMBASE, Cochrane database, and reference lists of retrieved studies. Controlled, clinical, English-language studies exploring the diagnostic and monitoring value of VOCs in asthma, COPD, CF, lung cancer and respiratory tract infections were included. Data on study design, setting, participant characteristics, VOCs techniques, and outcome measures were extracted. Seventy-three studies were included, counting in total 3,952 patients and 2,973 healthy controls. The collection and analysis of exhaled VOCs is non-invasive and could be easily applied in the broad range of patients, including subjects with severe disease and children. Various research groups demonstrated that VOCs profiles could accurately distinguish patients with a pulmonary disease from healthy controls. Pulmonary diseases seem to be characterized by a disease specific breath-print, as distinct profiles were found in patients with dissimilar diseases. The heterogeneity of studies challenged the inter-laboratory comparability. In conclusion, profiles of VOCs are potentially able to accurately diagnose various pulmonary diseases. Despite these promising findings, multiple challenges such as further standardization and validation of the diverse techniques need to be mastered before VOCs can be applied into clinical practice.},
	language = {en},
	number = {1},
	urldate = {2019-05-20},
	journal = {Respiratory Research},
	author = {van de Kant, Kim DG and van der Sande, Linda JTM and Jöbsis, Quirijn and van Schayck, Onno CP and Dompeling, Edward},
	year = {2012},
	pages = {117},
	file = {van de Kant et al. - 2012 - Clinical use of exhaled volatile organic compounds.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\SJ8BB7YK\\van de Kant et al. - 2012 - Clinical use of exhaled volatile organic compounds.pdf:application/pdf}
}

@article{holzinger_ptrwid:_2015,
	title = {{PTRwid}: {A} new widget tool for processing {PTR}-{TOF}-{MS} data},
	volume = {8},
	issn = {1867-8548},
	shorttitle = {{PTRwid}},
	url = {https://www.atmos-meas-tech.net/8/3903/2015/},
	doi = {10.5194/amt-8-3903-2015},
	abstract = {PTRwid is a fast and user friendly tool that has been developed to process data from proton-transfer-reaction time-of-ﬂight mass spectrometers (PTR-TOF-MS) that use HTOF (high-resolution time-of-ﬂight) mass spectrometers from Tofwerk AG (Switzerland). PTRwid is designed for a comprehensive evaluation of whole laboratory or ﬁeld-based studies. All processing runs autonomously, and entire laboratory or ﬁeld campaigns can, in principle, be processed with a few mouse clicks.},
	language = {en},
	number = {9},
	urldate = {2019-05-20},
	journal = {Atmospheric Measurement Techniques},
	author = {Holzinger, R.},
	month = sep,
	year = {2015},
	pages = {3903--3922},
	file = {Holzinger - 2015 - PTRwid A new widget tool for processing PTR-TOF-M.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\ZHGWTLG2\\Holzinger - 2015 - PTRwid A new widget tool for processing PTR-TOF-M.pdf:application/pdf}
}

@article{gohlke_early_1993,
	title = {Early gas chromatography/mass spectrometry},
	volume = {4},
	issn = {10440305},
	url = {http://link.springer.com/10.1016/1044-0305(93)85001-E},
	doi = {10.1016/1044-0305(93)85001-E},
	language = {en},
	number = {5},
	urldate = {2019-05-20},
	journal = {Journal of the American Society for Mass Spectrometry},
	author = {Gohlke, Roland S. and McLafferty, Fred W.},
	month = may,
	year = {1993},
	pages = {367--371},
	file = {Gohlke et McLafferty - 1993 - Early gas chromatographymass spectrometry.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\KHRQKEQK\\Gohlke et McLafferty - 1993 - Early gas chromatographymass spectrometry.pdf:application/pdf}
}

@article{wehinger_lung_2007,
	title = {Lung cancer detection by proton transfer reaction mass-spectrometric analysis of human breath gas},
	volume = {265},
	issn = {13873806},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1387380607002382},
	doi = {10.1016/j.ijms.2007.05.012},
	abstract = {Background: Determination of the diagnostic usefulness of proton transfer reaction mass spectrometry (PTR-MS) for detecting primary lung cancer through analysis of volatile organic compounds (VOCs) in exhaled human breath was demonstrated in this investigation. Unlike, for example, gas-chromatographic analyses, PTR-MS can be used without time-consuming preconcentration of the gas samples.
Methods: By means of PTR-MS, exhaled breath samples from primary lung cancer patients (n = 17) were analyzed and compared with both an overall control collective (controls total, n = 170) and three sub-collectives: hospital personnel (controls hospital, n = 35), age-matched persons (controls age, n = 25), and smokers (controls s, n = 60), respectively.
Results: Among the VOCs present at reasonably high concentrations, the ones leading to the product ion at m/z = 31 (VOC-31, tentatively protonated formaldehyde) and m/z = 43 (VOC-43, tentatively a fragment of protonated iso-propanol), were found at signiﬁcantly higher concentrations in the breath gas of the primary lung cancer patients as compared to the healthy controls at the following median concentrations (with interquartile distance, iqr): For VOC-31 the median concentrations were 7.0 ppb (iqr, 15.5 ppb) versus 3.0 ppb (iqr, 1.9 ppb) with P {\textless} 10−4. For VOC-43 the median concentrations were 244.1 ppb (iqr, 236.2 ppb) versus 94.1 ppb (iqr, 55.2 ppb) with P {\textless} 10−6. The discriminative power between the two collectives was further assessed by ROC-curves obtained upon variation of the chosen threshold concentration and by Fisher’s Quadratic Discriminant Method.
Conclusions: Within the limits of pilot study, VOC-31 and -43 were found to best discriminate between exhaled breath of primary lung cancer cases and healthy controls. Simple and time-saving breath gas analysis by PTR-MS makes this method attractive for a larger clinical evaluation. It may become a new valuable tool for diagnosing primary lung cancer.},
	language = {en},
	number = {1},
	urldate = {2019-05-20},
	journal = {International Journal of Mass Spectrometry},
	author = {Wehinger, Andreas and Schmid, Alex and Mechtcheriakov, Sergei and Ledochowski, Maximilian and Grabmer, Christoph and Gastl, Guenther A. and Amann, Anton},
	month = aug,
	year = {2007},
	pages = {49--59},
	annote = {Off line : l'air expirée est collectée dans un sac de 3L, ainsi que l'air ambiant 
les sac sont "nettoyé"
le sepctre est traité avec MATLAB ( masse 21-201)
selectionne uniquement les VOC : tq :
(inspiratory concentration)i≤ 0.6(expiratory concentration)i.
alternative apporche :
expiratory concentration − inspiratory concentration
on prend pas en compte les intensité négative},
	file = {Wehinger et al. - 2007 - Lung cancer detection by proton transfer reaction .pdf:C\:\\Users\\CR258086\\Zotero\\storage\\2C4FYU6S\\Wehinger et al. - 2007 - Lung cancer detection by proton transfer reaction .pdf:application/pdf}
}

@article{bajtarevic_noninvasive_2009,
	title = {Noninvasive detection of lung cancer by analysis of exhaled breath},
	volume = {9},
	issn = {1471-2407},
	url = {http://bmccancer.biomedcentral.com/articles/10.1186/1471-2407-9-348},
	doi = {10.1186/1471-2407-9-348},
	language = {en},
	number = {1},
	urldate = {2019-05-20},
	journal = {BMC Cancer},
	author = {Bajtarevic, Amel and Ager, Clemens and Pienz, Martin and Klieber, Martin and Schwarz, Konrad and Ligor, Magdalena and Ligor, Tomasz and Filipiak, Wojciech and Denz, Hubert and Fiegl, Michael and Hilbe, Wolfgang and Weiss, Wolfgang and Lukas, Peter and Jamnig, Herbert and Hackl, Martin and Haidenberger, Alfred and Buszewski, Bogusław and Miekisch, Wolfram and Schubert, Jochen and Amann, Anton},
	month = dec,
	year = {2009},
	pages = {348},
	annote = {air expiré et ambient collecté dans un Tedlar
donnée filtrer : garde les molécule présente a moin 15\% de plus que dans l'air ambiant 
ajput GCMS analysis},
	file = {Bajtarevic et al. - 2009 - Noninvasive detection of lung cancer by analysis o.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\NGYD7JMU\\Bajtarevic et al. - 2009 - Noninvasive detection of lung cancer by analysis o.pdf:application/pdf}
}

@article{cristescu_screening_2011,
	title = {Screening for emphysema via exhaled volatile organic compounds},
	volume = {5},
	issn = {1752-7155, 1752-7163},
	url = {http://stacks.iop.org/1752-7163/5/i=4/a=046009?key=crossref.c32325fed4ac4e42a95c31b898674471},
	doi = {10.1088/1752-7155/5/4/046009},
	abstract = {Chronic obstructive pulmonary disease (COPD)/emphysema risk groups are well deﬁned and screening allows for early identiﬁcation of disease. The capability of exhaled volatile organic compounds (VOCs) to detect emphysema, as found by computed tomography (CT) in current and former heavy smokers participating in a lung cancer screening trial, was investigated. CT scans, pulmonary function tests and breath sample collections were obtained from 204 subjects. Breath samples were analyzed with a proton-transfer reaction mass spectrometer (PTR-MS) to obtain VOC proﬁles listed as ions at various mass-to-charge ratios (m/z). Using bootstrapped stepwise forward logistic regression, we identiﬁed speciﬁc breath proﬁles as a potential tool for the diagnosis of emphysema, of airﬂow limitation or gas-exchange impairment. A marker for emphysema was found at m/z 87 (tentatively attributed to 2-methylbutanal). The area under the receiver operating characteristic curve (ROC) of this marker to diagnose emphysema was 0.588 (95\% CI 0.453–0.662). Mass-to-charge ratios m/z 52 (most likely chloramine) and m/z 135 (alkyl benzene) were linked to obstructive disease and m/z 122 (most probably alkyl homologs) to an impaired diffusion capacity. ROC areas were 0.646 (95\% CI 0.562–0.730) and 0.671 (95\% CI 0.524–0.710), respectively. In the screening setting, exhaled VOCs measured by PTR-MS constitute weak markers for emphysema, pulmonary obstruction and impaired diffusion capacity.},
	language = {en},
	number = {4},
	urldate = {2019-05-20},
	journal = {Journal of Breath Research},
	author = {Cristescu, S M and Gietema, H A and Blanchet, L and Kruitwagen, C L J J and Munnik, P and van Klaveren, R J and Lammers, J W J and Buydens, L and Harren, F J M and Zanen, P},
	month = dec,
	year = {2011},
	pages = {046009},
	file = {Cristescu et al. - 2011 - Screening for emphysema via exhaled volatile organ.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\IMZKI4WX\\Cristescu et al. - 2011 - Screening for emphysema via exhaled volatile organ.pdf:application/pdf}
}

@article{steeghs_off-line_2007,
	title = {An off-line breath sampling and analysis method suitable for large screening studies},
	volume = {28},
	issn = {0967-3334, 1361-6579},
	url = {http://stacks.iop.org/0967-3334/28/i=5/a=005?key=crossref.0f94ae95edcd44e4ba74fd34b771c8cd},
	doi = {10.1088/0967-3334/28/5/005},
	abstract = {We present a new, off-line breath collection and analysis method, suitable for large screening studies. The breath collection system is based on the guidelines of the American Thoracic Society for the sampling of exhaled NO. Breath containing volatile gases is collected in custom-made black-layered Tedlar bags and analyzed by proton-transfer reaction mass spectrometry (PTR-MS). The collection method and data analysis is validated for its accuracy, precision, selectivity, limits of detection, sensitivity and reproducibility. Consecutive ﬁllings of ﬁve bags by the same person gave reproducible results to within 12\% relative standard deviation (RSD) for methanol, acetaldehyde, acetone and water content from breath, whereas isoprene was constant to within 30\% RSD. In an exploratory small-scale case-control study, we monitor the exhaled breath of 11 lung cancer patients on the day before surgery. The control group consisted of 57 age-matched subjects, the so-called ‘healthy smokers’. This study is used as an example of the use of the system presented here.},
	language = {en},
	number = {5},
	urldate = {2019-05-20},
	journal = {Physiological Measurement},
	author = {Steeghs, M M L and Cristescu, S M and Munnik, P and Zanen, P and Harren, F J M},
	month = may,
	year = {2007},
	pages = {503--514},
	file = {Steeghs et al. - 2007 - An off-line breath sampling and analysis method su.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\RDZ9PT2S\\Steeghs et al. - 2007 - An off-line breath sampling and analysis method su.pdf:application/pdf}
}

@article{zhou_exhaled_2017,
	title = {Exhaled breath online measurement for cervical cancer patients and healthy subjects by proton transfer reaction mass spectrometry},
	volume = {409},
	issn = {1618-2642, 1618-2650},
	url = {http://link.springer.com/10.1007/s00216-017-0498-0},
	doi = {10.1007/s00216-017-0498-0},
	language = {en},
	number = {23},
	urldate = {2019-05-20},
	journal = {Analytical and Bioanalytical Chemistry},
	author = {Zhou, Wenzhao and Huang, Chaoqun and Zou, Xue and Lu, Yan and Shen, Chengyin and Ding, Xiping and Wang, Hongzhi and Jiang, Haihe and Chu, Yannan},
	month = sep,
	year = {2017},
	pages = {5603--5612},
	file = {Zhou et al. - 2017 - Exhaled breath online measurement for cervical can.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\SDGVBJIL\\Zhou et al. - 2017 - Exhaled breath online measurement for cervical can.pdf:application/pdf}
}

@article{zou_exhaled_2016,
	title = {Exhaled gases online measurements for esophageal cancer patients and healthy people by proton transfer reaction mass spectrometry: {Exhaled} gas esophageal cancer {PTR}-{MS}},
	volume = {31},
	issn = {08159319},
	shorttitle = {Exhaled gases online measurements for esophageal cancer patients and healthy people by proton transfer reaction mass spectrometry},
	url = {http://doi.wiley.com/10.1111/jgh.13380},
	doi = {10.1111/jgh.13380},
	abstract = {Background: Esophageal cancer is a prevalent malignancy. There is a considerable demand for developing a fast and noninvasive method to screen out the suspect esophageal cancer patients who may undergo further clinical diagnosis.
Methods: The exhaled breathes from 29 esophageal cancer patients and 57 healthy people were directly measured using our home-made proton transfer reaction mass spectrometer (PTR-MS). Mann-Whitney U test and stepwise discriminant analysis were applied to identify the ions in the breath mass spectral data which can distinguish cancer cohort from healthy group. Receiver operating characteristics (ROC) analysis was also performed.
Results: Seven kinds of ions in the breath mass spectrum, viz., m/z 136, m/z 34, m/z 63, m/z 27, m/z 95, m/z 107 and m/z 45, have been found to distinguish between the esophageal cancer patients and healthy people with a sensitivity of 86.2\% and a speciﬁcity of 89.5\%, respectively. Compared with that from the healthy people, the breath mass spectra from esophageal cancer patients show that the mediant intensities of ﬁve kinds of ions were decrease and the rest two kinds of ions were increase. ROC analysis gave the area under the curve (AUC) of 0.943.
Conclusions: This pilot study shows that the ionic characteristics of exhaled VOCs detected by PTR-MS may be used to differentiate between the esophageal cancer patients and the healthy people. Although the breath tests for more patients are needed to conﬁrm such results, the present work indicates that the PTR-MS may be a promising method in the esophageal cancer screening.},
	language = {en},
	number = {11},
	urldate = {2019-05-20},
	journal = {Journal of Gastroenterology and Hepatology},
	author = {Zou, Xue and Zhou, Wenzhao and Lu, Yan and Shen, Chengyin and Hu, Zongtao and Wang, Hongzhi and Jiang, Haihe and Chu, Yannan},
	month = nov,
	year = {2016},
	pages = {1837--1843},
	file = {Zou et al. - 2016 - Exhaled gases online measurements for esophageal c.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\WWUJJ33J\\Zou et al. - 2016 - Exhaled gases online measurements for esophageal c.pdf:application/pdf}
}

@article{huang_real-time_2016,
	title = {Real-time monitoring of respiratory absorption factors of volatile organic compounds in ambient air by proton transfer reaction time-of-flight mass spectrometry},
	volume = {320},
	issn = {03043894},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0304389416307889},
	doi = {10.1016/j.jhazmat.2016.08.064},
	language = {en},
	urldate = {2019-05-21},
	journal = {Journal of Hazardous Materials},
	author = {Huang, Zhonghui and Zhang, Yanli and Yan, Qiong and Zhang, Zhou and Wang, Xinming},
	month = dec,
	year = {2016},
	pages = {547--555},
	annote = {Utilise PTR Viewver de ionicon
air expiré par le nez puis bloque l'entrée
analyse ciblée sur BTEX (

Benzène B
Toluène T
Éthylbenzène E
Xylènes X)
tracer d'expiration : isoprene

utilise un buffer},
	file = {Huang et al. - 2016 - Real-time monitoring of respiratory absorption fac.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\4RGK7TLK\\Huang et al. - 2016 - Real-time monitoring of respiratory absorption fac.pdf:application/pdf}
}

@article{morisco_rapid_2013,
	title = {Rapid “{Breath}-{Print}” of {Liver} {Cirrhosis} by {Proton} {Transfer} {Reaction} {Time}-of-{Flight} {Mass} {Spectrometry}. {A} {Pilot} {Study}.},
	volume = {8},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0059658},
	doi = {10.1371/journal.pone.0059658},
	abstract = {The aim of the present work was to test the potential of Proton Transfer Reaction Time-of-Flight Mass Spectrometry (PTRToF-MS) in the diagnosis of liver cirrhosis and the assessment of disease severity by direct analysis of exhaled breath. Twenty-six volunteers have been enrolled in this study: 12 patients (M/F 8/4, mean age 70.5 years, min-max 42–80 years) with liver cirrhosis of different etiologies and at different severity of disease and 14 healthy subjects (M/F 5/9, mean age 52.3 years, min-max 35–77 years). Real time breath analysis was performed on fasting subjects using a buffered end-tidal on-line sampler directly coupled to a PTR-ToF-MS. Twelve volatile organic compounds (VOCs) resulted significantly differently in cirrhotic patients (CP) compared to healthy controls (CTRL): four ketones (2-butanone, 2- or 3- pentanone, C8-ketone, C9ketone), two terpenes (monoterpene, monoterpene related), four sulphur or nitrogen compounds (sulfoxide-compound, Scompound, NS-compound, N-compound) and two alcohols (heptadienol, methanol). Seven VOCs (2-butanone, C8-ketone, a monoterpene, 2,4-heptadienol and three compounds containing N, S or NS) resulted significantly differently in compensate cirrhotic patients (Child-Pugh A; CP-A) and decompensated cirrhotic subjects (Child-Pugh B+C; CP-B+C). ROC (Receiver Operating Characteristic) analysis was performed considering three contrast groups: CP vs CTRL, CP-A vs CTRL and CP-A vs CP-B+C. In these comparisons monoterpene and N-compound showed the best diagnostic performance.},
	language = {en},
	number = {4},
	urldate = {2019-05-21},
	journal = {PLoS ONE},
	author = {Morisco, Filomena and Aprea, Eugenio and Lembo, Vincenzo and Fogliano, Vincenzo and Vitaglione, Paola and Mazzone, Giovanna and Cappellin, Luca and Gasperi, Flavia and Masone, Stefania and De Palma, Giovanni Domenico and Marmo, Riccardo and Caporaso, Nicola and Biasioli, Franco},
	editor = {Haybaeck, Johannes},
	month = apr,
	year = {2013},
	pages = {e59658},
	file = {Morisco et al. - 2013 - Rapid “Breath-Print” of Liver Cirrhosis by Proton .pdf:C\:\\Users\\CR258086\\Zotero\\storage\\REXT27M5\\Morisco et al. - 2013 - Rapid “Breath-Print” of Liver Cirrhosis by Proton .pdf:application/pdf}
}

@article{lindinger_-line_1998,
	title = {On-line monitoring of volatile organic compounds at pptv levels by means of proton-transfer-reaction mass spectrometry ({PTR}-{MS}) medical applications, food control and environmental research},
	volume = {173},
	issn = {01681176},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0168117697002814},
	doi = {10.1016/S0168-1176(97)00281-4},
	abstract = {A proton transfer reaction mass spectrometer (PTR-MS) system has been developed which allows for on-line measurements of trace components with concentrations as low as a few pptv. The method is based on reactions of H 30 + ions, which perform non-dissociative proton transfer to most of the common volatile organic compounds (VOCs) but do not react with any of the components present in clean air. Medical applications by means of breath analysis allow for monitoring of metabolic processes in the human body, and examples of food research are discussed on the basis of VOC emissions from fruit, coffee and meat. Environmental applications include investigations of VOC emissions from decaying biomatter which have been found to be an important source for tropospheric acetone, methanol and ethanol. On-line monitoring of the diurnal variations of VOCs in the troposphere yield data demonstrating the present sensitivity of PTR-MS to be in the range of a few pptv. Finally, PTR-MS has proven to be an ideal tool to measure Henry's law constants and their dependencies on temperature as well as on the salt content of water. © 1998 Elsevier Science B.V.},
	language = {en},
	number = {3},
	urldate = {2019-05-21},
	journal = {International Journal of Mass Spectrometry and Ion Processes},
	author = {Lindinger, W. and Hansel, A. and Jordan, A.},
	month = feb,
	year = {1998},
	pages = {191--241},
	file = {Lindinger et al. - 1998 - On-line monitoring of volatile organic compounds a.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\354VDJEX\\Lindinger et al. - 1998 - On-line monitoring of volatile organic compounds a.pdf:application/pdf}
}

@article{pleil_advances_2019,
	title = {Advances in proton transfer reaction mass spectrometry ({PTR}-{MS}): applications in exhaled breath analysis, food science, and atmospheric chemistry},
	issn = {1752-7155, 1752-7163},
	shorttitle = {Advances in proton transfer reaction mass spectrometry ({PTR}-{MS})},
	url = {http://iopscience.iop.org/article/10.1088/1752-7163/ab21a7},
	doi = {10.1088/1752-7163/ab21a7},
	language = {en},
	urldate = {2019-05-22},
	journal = {Journal of Breath Research},
	author = {Pleil, Joachim D and Hansel, A and Beauchamp, Jonathan D},
	month = may,
	year = {2019},
	file = {Pleil et al. - 2019 - Advances in proton transfer reaction mass spectrom.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\PM2A6RTX\\Pleil et al. - 2019 - Advances in proton transfer reaction mass spectrom.pdf:application/pdf}
}

@article{aprea_application_2014,
	title = {Application of {PTR}-{TOF}-{MS} to investigate metabolites in exhaled breath of patients affected by coeliac disease under gluten free diet},
	volume = {966},
	issn = {15700232},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S157002321400097X},
	doi = {10.1016/j.jchromb.2014.02.015},
	abstract = {Coeliac disease (CD) is a common chronic inﬂammatory disorder of the small bowel induced in genetically susceptible people by the exposure to gliadin gluten. Even though several tests are available to assist the diagnosis, CD remains a biopsy-deﬁned disorder, thus any non-invasive or less invasive diagnostic tool may be beneﬁcial. The analysis of volatile metabolites in exhaled breath, given its non-invasive nature, is particularly promising as a screening tool of disease in symptomatic or non-symptomatic patients.},
	language = {en},
	urldate = {2019-05-22},
	journal = {Journal of Chromatography B},
	author = {Aprea, Eugenio and Cappellin, Luca and Gasperi, Flavia and Morisco, Filomena and Lembo, Vincenzo and Rispo, Antonio and Tortora, Raffaella and Vitaglione, Paola and Caporaso, Nicola and Biasioli, Franco},
	month = sep,
	year = {2014},
	pages = {208--213},
	file = {Aprea et al. - 2014 - Application of PTR-TOF-MS to investigate metabolit.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\5VNBKDQ6\\Aprea et al. - 2014 - Application of PTR-TOF-MS to investigate metabolit.pdf:application/pdf}
}

@book{hansel_8th_2019,
	title = {8th {International} {Conference} on {Proton} {Transfer} {Reaction} {Mass} {Spectrometry} and its {Applications} ({PTRMS} 2019).},
	isbn = {978-3-903187-46-7},
	language = {en},
	author = {Hansel, Armin and Dunkl, Jürgen and {Universität Innsbruck} and {innsbruck university press iup}},
	year = {2019},
	note = {OCLC: 1101344546},
	file = {Hansel et al. - 2019 - 8th International Conference on Proton Transfer Re.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\SR8BIS5V\\Hansel et al. - 2019 - 8th International Conference on Proton Transfer Re.pdf:application/pdf}
}

@article{williams_cinema_2016,
	title = {Cinema audiences reproducibly vary the chemical composition of air during films, by broadcasting scene specific emissions on breath},
	volume = {6},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/srep25464},
	doi = {10.1038/srep25464},
	language = {en},
	number = {1},
	urldate = {2019-05-26},
	journal = {Scientific Reports},
	author = {Williams, Jonathan and Stönner, Christof and Wicker, Jörg and Krauter, Nicolas and Derstroff, Bettina and Bourtsoukidis, Efstratios and Klüpfel, Thomas and Kramer, Stefan},
	month = jul,
	year = {2016},
	pages = {25464},
	file = {Williams et al. - 2016 - Cinema audiences reproducibly vary the chemical co.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\X8V9SP2H\\Williams et al. - 2016 - Cinema audiences reproducibly vary the chemical co.pdf:application/pdf}
}

@article{homann_1._nodate,
	title = {1. {Berichterstatter}: {Prof}. {Dr}. {Jonathan} {Williams}},
	language = {de},
	author = {Hoﬀmann, Dr Thorsten},
	pages = {141},
	file = {Hoﬀmann - 1. Berichterstatter Prof. Dr. Jonathan Williams.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\3QS7NUQ7\\Hoﬀmann - 1. Berichterstatter Prof. Dr. Jonathan Williams.pdf:application/pdf}
}

@article{wilde_breath_2019,
	title = {Breath analysis by two-dimensional gas chromatography with dual flame ionisation and mass spectrometric detection – {Method} optimisation and integration within a large-scale clinical study},
	volume = {1594},
	issn = {00219673},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0021967319301311},
	doi = {10.1016/j.chroma.2019.02.001},
	abstract = {Precision medicine has spurred new innovations in molecular pathology leading to recent advances in the analysis of exhaled breath as a non-invasive diagnostic tool. Volatile organic compounds (VOCs) detected in exhaled breath have the potential to reveal a wealth of chemical and metabolomic information. This study describes the development of a method for the analysis of breath, based on automated thermal desorption (TD) combined with ﬂow modulated comprehensive two-dimensional gas chromatography (GC×GC) with dual ﬂame ionisation and quadrupole mass spectrometric detection (FID and qMS). The constrained optimisation and analytical protocol was designed to meet the practical demands of a largescale multi-site clinical study, while maintaining analytical rigour to produce high ﬁdelity data. The results demonstrate a comprehensive method optimisation for the collection and analysis of breath VOCs by GC×GC, integral to the standardisation and integration of breath analysis within large clinical studies. © 2019 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).},
	language = {en},
	urldate = {2019-05-26},
	journal = {Journal of Chromatography A},
	author = {Wilde, Michael J. and Cordell, Rebecca L. and Salman, Dahlia and Zhao, Bo and Ibrahim, Wadah and Bryant, Luke and Ruszkiewicz, Dorota and Singapuri, Amisha and Free, Robert C. and Gaillard, Erol A. and Beardsmore, Caroline and Thomas, C.L. Paul and Brightling, Chris E. and Siddiqui, Salman and Monks, Paul S.},
	month = jun,
	year = {2019},
	pages = {160--172},
	file = {Wilde et al. - 2019 - Breath analysis by two-dimensional gas chromatogra.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\NHLXAVJT\\Wilde et al. - 2019 - Breath analysis by two-dimensional gas chromatogra.pdf:application/pdf}
}

@article{sukul_instant_2015,
	title = {Instant effects of changing body positions on compositions of exhaled breath},
	volume = {9},
	issn = {1752-7163},
	url = {http://stacks.iop.org/1752-7163/9/i=4/a=047105?key=crossref.b3a3e383ff839d9cb9e5669d99853c04},
	doi = {10.1088/1752-7155/9/4/047105},
	abstract = {Concentrations of exhaled volatile organic compounds (VOCs) may depend not only on biochemical or pathologic processes but also on physiological parameters. As breath sampling may be done in different body positions, effects of the sampling position on exhaled VOC concentrations were investigated by means of real-time mass spectrometry. Breaths from 15 healthy volunteers were analyzed in real-time by PTR-ToF-MS-8000 during paced breathing (12/min) in a continuous side-stream mode. We applied two series of body positions (setup 1: sitting, standing, supine, and sitting; setup 2: supine, left lateral, right lateral, prone, and supine). Each position was held for 2 min. Breath VOCs were quantiﬁed in inspired and alveolar air by means of a custom-made algorithm. Parallel monitoring of hemodynamics and capnometry was performed noninvasively. In setup 1, when compared to the initial sitting position, normalized mean concentrations of isoprene, furan, and acetonitrile decreased by 24\%, 26\%, and 9\%, respectively, during standing and increased by 63\%, 36\%, and 10\% during lying mirroring time proﬁles of stroke volume and pETCO2. In contrast, acetone and H2S concentrations remained almost constant. In setup 2, when compared to the initial supine position, mean alveolar concentrations of isoprene and furan increased signiﬁcantly up to 29\% and 16\%, respectively, when position was changed from lying on the right side to the prone position. As cardiac output and stroke volume decreased at that time, the reasons for the observed concentrations changes have to be linked to the ventilation/ perfusion ratio or compartmental distribution rather than to perfusion alone. During ﬁnal postures, all VOC concentrations, hemodynamics, and pET-CO2 returned to baseline. Exhaled blood-borne VOC proﬁles changed due to body postures. Changes depended on cardiac stroke volume, origin, compartmental distribution and physico-chemical properties of the substances. Patients’ positions and cardiac output have to be controlled when concentrations of breath VOCs are to be interpreted in terms of biomarkers.},
	language = {en},
	number = {4},
	urldate = {2019-05-26},
	journal = {Journal of Breath Research},
	author = {Sukul, Pritam and Trefz, Phillip and Kamysek, Svend and Schubert, Jochen K and Miekisch, Wolfram},
	month = nov,
	year = {2015},
	pages = {047105},
	file = {Sukul et al. - 2015 - Instant effects of changing body positions on comp.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\ZQI4GPXD\\Sukul et al. - 2015 - Instant effects of changing body positions on comp.pdf:application/pdf}
}

@article{casas-ferreira_non-separative_2019,
	title = {Non-separative mass spectrometry methods for non-invasive medical diagnostics based on volatile organic compounds: {A} review},
	volume = {1045},
	issn = {00032670},
	shorttitle = {Non-separative mass spectrometry methods for non-invasive medical diagnostics based on volatile organic compounds},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0003267018308560},
	doi = {10.1016/j.aca.2018.07.005},
	abstract = {In this review, an assessment of non-separative methods based on mass spectrometry used to analyse volatile organic compounds in the ﬁeld of bioanalysis is performed. The use of non-separative methods based on mass spectrometry has been established as an attractive option for analysing compounds. These instrumental conﬁgurations are suitable for biomedical applications because of their versatility, rapid output of results, and the wide range of volatile organic compounds that can be determined.},
	language = {en},
	urldate = {2019-05-27},
	journal = {Analytica Chimica Acta},
	author = {Casas-Ferreira, Ana María and Nogal-Sánchez, Miguel del and Pérez-Pavón, José Luis and Moreno-Cordero, Bernardo},
	month = jan,
	year = {2019},
	pages = {10--22},
	file = {Casas-Ferreira et al. - 2019 - Non-separative mass spectrometry methods for non-i.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\5M77VLMR\\Casas-Ferreira et al. - 2019 - Non-separative mass spectrometry methods for non-i.pdf:application/pdf}
}

@article{amann_human_2014,
	title = {The human volatilome: volatile organic compounds ({VOCs}) in exhaled breath, skin emanations, urine, feces and saliva},
	volume = {8},
	issn = {1752-7155, 1752-7163},
	shorttitle = {The human volatilome},
	url = {http://stacks.iop.org/1752-7163/8/i=3/a=034001?key=crossref.6e7280a35b5e0d4fb0ad16f618f47439},
	doi = {10.1088/1752-7155/8/3/034001},
	language = {en},
	number = {3},
	urldate = {2019-05-27},
	journal = {Journal of Breath Research},
	author = {Amann, Anton and Costello, Ben de Lacy and Miekisch, Wolfram and Schubert, Jochen and Buszewski, Bogusław and Pleil, Joachim and Ratcliffe, Norman and Risby, Terence},
	month = jun,
	year = {2014},
	pages = {034001},
	file = {Amann et al. - 2014 - The human volatilome volatile organic compounds (.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\586TZJ7J\\Amann et al. - 2014 - The human volatilome volatile organic compounds (.pdf:application/pdf}
}

@article{smolinska_current_2014,
	title = {Current breathomics—a review on data pre-processing techniques and machine learning in metabolomics breath analysis},
	volume = {8},
	issn = {1752-7155, 1752-7163},
	url = {http://stacks.iop.org/1752-7163/8/i=2/a=027105?key=crossref.be9a7f376602cdf8a2717c5a9b326436},
	doi = {10.1088/1752-7155/8/2/027105},
	abstract = {We deﬁne breathomics as the metabolomics study of exhaled air. It is a strongly emerging metabolomics research ﬁeld that mainly focuses on health-related volatile organic compounds (VOCs). Since the amount of these compounds varies with health status, breathomics holds great promise to deliver non-invasive diagnostic tools. Thus, the main aim of breathomics is to ﬁnd patterns of VOCs related to abnormal (for instance inﬂammatory) metabolic processes occurring in the human body. Recently, analytical methods for measuring VOCs in exhaled air with high resolution and high throughput have been extensively developed. Yet, the application of machine learning methods for ﬁngerprinting VOC proﬁles in the breathomics is still in its infancy. Therefore, in this paper, we describe the current state of the art in data pre-processing and multivariate analysis of breathomics data. We start with the detailed pre-processing pipelines for breathomics data obtained from gas-chromatography mass spectrometry and an ion-mobility spectrometer coupled to multi-capillary columns. The outcome of data pre-processing is a matrix containing the relative abundances of a set of VOCs for a group of patients under different conditions (e.g. disease stage, treatment). Independently of the utilized analytical method, the most important question, ‘which VOCs are discriminatory?’, remains the same. Answers can be given by several modern machine learning techniques (multivariate statistics) and, therefore, are the focus of this paper. We demonstrate the advantages as well the drawbacks of such techniques. We aim to help the community to understand how to proﬁt from a particular method. In parallel, we hope to make the community aware of the existing data fusion methods, as yet unresearched in breathomics.},
	language = {en},
	number = {2},
	urldate = {2019-05-27},
	journal = {Journal of Breath Research},
	author = {Smolinska, A and Hauschild, A-Ch and Fijten, R R R and Dallinga, J W and Baumbach, J and van Schooten, F J},
	month = apr,
	year = {2014},
	pages = {027105},
	file = {Smolinska et al. - 2014 - Current breathomics—a review on data pre-processin.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\B2IH47IP\\Smolinska et al. - 2014 - Current breathomics—a review on data pre-processin.pdf:application/pdf}
}

@article{wee_continuous_2008,
	title = {A continuous wavelet transform algorithm for peak detection},
	volume = {29},
	issn = {01730835, 15222683},
	url = {http://doi.wiley.com/10.1002/elps.200800096},
	doi = {10.1002/elps.200800096},
	language = {en},
	number = {20},
	urldate = {2019-05-29},
	journal = {ELECTROPHORESIS},
	author = {Wee, Andrew and Grayden, David B. and Zhu, Yonggang and Petkovic-Duran, Karolina and Smith, David},
	month = nov,
	year = {2008},
	pages = {4215--4225},
	file = {Wee et al. - 2008 - A continuous wavelet transform algorithm for peak .pdf:C\:\\Users\\CR258086\\Zotero\\storage\\MNF3F2IS\\Wee et al. - 2008 - A continuous wavelet transform algorithm for peak .pdf:application/pdf}
}

@article{morris_bayesian_2008,
	title = {Bayesian {Analysis} of {Mass} {Spectrometry} {Proteomic} {Data} {Using} {Wavelet}-{Based} {Functional} {Mixed} {Models}},
	volume = {64},
	issn = {0006341X},
	url = {http://doi.wiley.com/10.1111/j.1541-0420.2007.00895.x},
	doi = {10.1111/j.1541-0420.2007.00895.x},
	abstract = {In this article, we apply the recently developed Bayesian wavelet-based functional mixed model methodology to analyze MALDI-TOF mass spectrometry proteomic data. By modeling mass spectra as functions, this approach avoids reliance on peak detection methods. The ﬂexibility of this framework in modeling nonparametric ﬁxed and random eﬀect functions enables it to model the eﬀects of multiple factors simultaneously, allowing one to perform inference on multiple factors of interest using the same model ﬁt, while adjusting for clinical or experimental covariates that may aﬀect both the intensities and locations of peaks in the spectra. For example, this provides a straightforward way to account for systematic block and batch eﬀects that characterize these data. From the model output, we identify spectral regions that are diﬀerentially expressed across experimental conditions, in a way that takes both statistical and clinical signiﬁcance into account and controls the Bayesian false discovery rate to a prespeciﬁed level. We apply this method to two cancer studies.},
	language = {en},
	number = {2},
	urldate = {2019-05-29},
	journal = {Biometrics},
	author = {Morris, Jeffrey S. and Brown, Philip J. and Herrick, Richard C. and Baggerly, Keith A. and Coombes, Kevin R.},
	month = jun,
	year = {2008},
	pages = {479--489},
	file = {Morris et al. - 2008 - Bayesian Analysis of Mass Spectrometry Proteomic D.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\B8AMMI5G\\Morris et al. - 2008 - Bayesian Analysis of Mass Spectrometry Proteomic D.pdf:application/pdf}
}

@article{fan_2-d_2009,
	title = {A 2-{D} continuous wavelet transform of mode shape data for damage detection of plate structures},
	volume = {46},
	issn = {00207683},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0020768309003308},
	doi = {10.1016/j.ijsolstr.2009.08.022},
	abstract = {A two-dimensional (2-D) continuous wavelet transform (CWT)-based damage detection algorithm using ‘‘Dergauss2d” wavelet for plate-type structures is presented. The 2-D CWT considered in this study is based on the formulation by Antoine et al. (2004). A concept of isosurface of 2-D wavelet coefﬁcients is proposed, and it is generated to indicate the location and approximate shape or area of the damage. The proposed algorithm is a response-based damage detection technique which only requires the mode shapes of the damaged plates. This algorithm is applied to the numerical vibration mode shapes of a cantilever plate with different types of damage to illustrate its effectiveness and viability. A comparative study with other two 2-D damage detection algorithms, i.e., 2-D gapped smoothing method (GSM) and 2-D strain energy method (SEM), is performed, and it demonstrates that the proposed 2-D CWT-based algorithm is superior in noise immunity and robust with limited sensor data. The algorithm is further implemented in an experimental modal test to detect impact damage in an FRP composite plate using smart piezoelectric actuators and sensors, demonstrating its applicability to the experimental mode shapes. The present 2-D CWT-based algorithm is among a few limited studies in the literature to explore the application of 2-D wavelets in damage detection, and as demonstrated in this study, it can be used as a viable and effective technique for damage identiﬁcation of plate- or shell-type structures.},
	language = {en},
	number = {25-26},
	urldate = {2019-05-29},
	journal = {International Journal of Solids and Structures},
	author = {Fan, Wei and Qiao, Pizhong},
	month = dec,
	year = {2009},
	pages = {4379--4395},
	file = {Fan et Qiao - 2009 - A 2-D continuous wavelet transform of mode shape d.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\58EXQF5X\\Fan et Qiao - 2009 - A 2-D continuous wavelet transform of mode shape d.pdf:application/pdf}
}

@article{garrett_common_nodate,
	title = {A {Common} {Sense} {Approach} to {Peak} {Picking} in {Two}-, {Three}-, and {Four}-{Dimensional} {Spectra} {Using} {Automatic} {Computer} {Analysis} of {Contour} {Diagrams}},
	language = {en},
	author = {Garrett, Daniel S and Powers, Robert and Gronenborn, Angela M and Clore, G Marius},
	pages = {8},
	file = {Garrett et al. - A Common Sense Approach to Peak Picking in Two-, T.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\L667GWK2\\Garrett et al. - A Common Sense Approach to Peak Picking in Two-, T.pdf:application/pdf}
}

@article{antoine_two-dimensional_1996,
	title = {Two-dimensional directional wavelets and the scale-angle representation},
	volume = {52},
	issn = {01651684},
	url = {https://linkinghub.elsevier.com/retrieve/pii/0165168496000655},
	doi = {10.1016/0165-1684(96)00065-5},
	abstract = {The two-dimensional continuous wavelet transform (CWT) is characterized by a rotation parameter, in addition to the usual translations and dilations. This enables it to detect edges and directions in images, provided a directional wavelet is used. First we briefly review the general properties of the 2-D CWT and describe several classes of wavelets, including the directional ones. Then we turn to the problem of wavelet calibration. We show, in particular, how the reproducing kernel may be used for defining and evaluating the scale and angle-resolving power of a wavelet. Finally, we illustrate the usefulness of the scale-angle representation of the CWT on the problem of disentangling a train of damped plane waves.},
	language = {en},
	number = {3},
	urldate = {2019-05-29},
	journal = {Signal Processing},
	author = {Antoine, J.-P. and Murenzi, R.},
	month = aug,
	year = {1996},
	pages = {259--281},
	file = {Antoine et Murenzi - 1996 - Two-dimensional directional wavelets and the scale.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\GZH2XPI7\\Antoine et Murenzi - 1996 - Two-dimensional directional wavelets and the scale.pdf:application/pdf}
}

@article{lindinger_-line_1998-1,
	title = {On-line monitoring of volatile organic compounds at pptv levels by means of proton-transfer-reaction mass spectrometry ({PTR}-{MS}) medical applications, food control and environmental research},
	volume = {173},
	issn = {01681176},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0168117697002814},
	doi = {10.1016/S0168-1176(97)00281-4},
	abstract = {A proton transfer reaction mass spectrometer (PTR-MS) system has been developed which allows for on-line measurements of trace components with concentrations as low as a few pptv. The method is based on reactions of H 30 + ions, which perform non-dissociative proton transfer to most of the common volatile organic compounds (VOCs) but do not react with any of the components present in clean air. Medical applications by means of breath analysis allow for monitoring of metabolic processes in the human body, and examples of food research are discussed on the basis of VOC emissions from fruit, coffee and meat. Environmental applications include investigations of VOC emissions from decaying biomatter which have been found to be an important source for tropospheric acetone, methanol and ethanol. On-line monitoring of the diurnal variations of VOCs in the troposphere yield data demonstrating the present sensitivity of PTR-MS to be in the range of a few pptv. Finally, PTR-MS has proven to be an ideal tool to measure Henry's law constants and their dependencies on temperature as well as on the salt content of water. © 1998 Elsevier Science B.V.},
	language = {en},
	number = {3},
	urldate = {2019-06-18},
	journal = {International Journal of Mass Spectrometry and Ion Processes},
	author = {Lindinger, W. and Hansel, A. and Jordan, A.},
	month = feb,
	year = {1998},
	pages = {191--241},
	file = {Lindinger et al. - 1998 - On-line monitoring of volatile organic compounds a.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\E4E84KKG\\Lindinger et al. - 1998 - On-line monitoring of volatile organic compounds a.pdf:application/pdf}
}

@article{du_improved_2006,
	title = {Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching},
	volume = {22},
	issn = {1367-4803, 1460-2059},
	url = {https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btl355},
	doi = {10.1093/bioinformatics/btl355},
	abstract = {Motivation: A major problem for current peak detection algorithms is that noise in mass spectrometry (MS) spectra gives rise to a high rate of false positives. The false positive rate is especially problematic in detecting peaks with low amplitudes. Usually, various baseline correction algorithms and smoothing methods are applied before attempting peak detection. This approach is very sensitive to the amount of smoothing and aggressiveness of the baseline correction, which contribute to making peak detection results inconsistent between runs, instrumentation and analysis methods.},
	language = {en},
	number = {17},
	urldate = {2019-06-28},
	journal = {Bioinformatics},
	author = {Du, P. and Kibbe, W. A. and Lin, S. M.},
	month = sep,
	year = {2006},
	pages = {2059--2065},
	file = {Du et al. - 2006 - Improved peak detection in mass spectrum by incorp.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\HL5BH72Q\\Du et al. - 2006 - Improved peak detection in mass spectrum by incorp.pdf:application/pdf}
}

@book{nason_wavelet_2008,
	address = {New York ; London},
	series = {Use {R}!},
	title = {Wavelet methods in statistics with {R}},
	isbn = {978-0-387-75960-9},
	language = {en},
	publisher = {Springer},
	author = {Nason, G. P.},
	year = {2008},
	note = {OCLC: ocn226974715},
	keywords = {Mathematical statistics, R (Computer program language), Wavelets (Mathematics)},
	file = {Nason - 2008 - Wavelet methods in statistics with R.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\DD2IZEIE\\Nason - 2008 - Wavelet methods in statistics with R.pdf:application/pdf}
}

@book{mallat_wavelet_2009,
	address = {Amsterdam ; Boston},
	edition = {3rd ed},
	title = {A wavelet tour of signal processing: the sparse way},
	isbn = {978-0-12-374370-1},
	shorttitle = {A wavelet tour of signal processing},
	language = {en},
	publisher = {Elsevier/Academic Press},
	author = {Mallat, S. G.},
	year = {2009},
	keywords = {Wavelets (Mathematics), Mathematics, Signal processing},
	file = {Mallat - 2009 - A wavelet tour of signal processing the sparse wa.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\PNGCIG9C\\Mallat - 2009 - A wavelet tour of signal processing the sparse wa.pdf:application/pdf}
}

@article{muller_new_2013-1,
	title = {A new software tool for the analysis of high resolution {PTR}-{TOF} mass spectra},
	volume = {127},
	issn = {01697439},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0169743913001275},
	doi = {10.1016/j.chemolab.2013.06.011},
	abstract = {The High Resolution Proton-Transfer-Reaction Time-of-Flight Mass Spectrometer (HR PTR-TOF-MS) is a powerful analytical tool used by various scientiﬁc communities for real-time measurements of volatile organic compounds (VOC). The analysis of HR PTR-TOF-MS data is, however, particularly demanding because of the large amount of complex data being generated. Based on recently developed or described mathematical methods, we have produced a new software tool, the PTR-TOF Data Analyzer, which greatly facilitates the data analysis process. The new software solution allows for i) a combined Poisson counting statistics and dead time correction of ion count rates, ii) accurate mass axis calibration, iii) an iterative residual peak analysis that detects up to 5 isobaric peaks per unit m/z, iv) time series analysis of both low and high mass and time resolution data and v) visualization of analysis results for fast quality assurance checks. After having been successfully tested by a group of users with different application needs, the PTR-TOF Data Analyzer is made generally available to the scientiﬁc community. This will improve the user-friendliness of the PTR-TOF-MS technique and facilitate scientiﬁc work with this new analytical mass spectrometer.},
	language = {en},
	urldate = {2019-01-31},
	journal = {Chemometrics and Intelligent Laboratory Systems},
	author = {Müller, Markus and Mikoviny, Tomáš and Jud, Werner and D'Anna, Barbara and Wisthaler, Armin},
	month = aug,
	year = {2013},
	pages = {158--165},
	file = {Müller et al. - 2013 - A new software tool for the analysis of high resol.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\NURUTGMG\\Müller et al. - 2013 - A new software tool for the analysis of high resol.pdf:application/pdf}
}

@article{griffin_snip_nodate,
	title = {snip, a statistics-sensitive background treatment for the quantitative analysis of pixe spectfta in geoscience applications},
	language = {en},
	author = {Griffin, W L and Sie, S H and Clayton, E},
	pages = {7},
	file = {If et al. - SNIP, A STATISTICS-SENSITIVE BACKGROUND TREATMENT .pdf:C\:\\Users\\CR258086\\Zotero\\storage\\98MLHXGE\\If et al. - SNIP, A STATISTICS-SENSITIVE BACKGROUND TREATMENT .pdf:application/pdf}
}

@article{savitzky_smoothing_1964-1,
	title = {Smoothing and {Differentiation} of {Data} by {Simplified} {Least} {Squares} {Procedures}.},
	volume = {36},
	issn = {0003-2700, 1520-6882},
	url = {http://pubs.acs.org/doi/abs/10.1021/ac60214a047},
	doi = {10.1021/ac60214a047},
	language = {en},
	number = {8},
	urldate = {2019-03-05},
	journal = {Analytical Chemistry},
	author = {Savitzky, Abraham. and Golay, M. J. E.},
	month = jul,
	year = {1964},
	pages = {1627--1639},
	file = {Savitzky et Golay - 1964 - Smoothing and Differentiation of Data by Simplifie.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\J27MZB38\\Savitzky et Golay - 1964 - Smoothing and Differentiation of Data by Simplifie.pdf:application/pdf}
}

@article{vivo-truyols_automatic_2006-1,
	title = {Automatic {Selection} of {Optimal} {Savitzky}−{Golay} {Smoothing}},
	volume = {78},
	issn = {0003-2700, 1520-6882},
	url = {https://pubs.acs.org/doi/10.1021/ac0600196},
	doi = {10.1021/ac0600196},
	language = {en},
	number = {13},
	urldate = {2019-03-06},
	journal = {Analytical Chemistry},
	author = {Vivó-Truyols, Gabriel and Schoenmakers, Peter J.},
	month = jul,
	year = {2006},
	pages = {4598--4608},
	file = {Vivó-Truyols et Schoenmakers - 2006 - Automatic Selection of Optimal Savitzky−Golay Smoo.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\7ZCWP8UX\\Vivó-Truyols et Schoenmakers - 2006 - Automatic Selection of Optimal Savitzky−Golay Smoo.pdf:application/pdf}
}

@article{langue_analysis_2008,
	title = {Analysis of mass spectrometric data: peak picking and map alignment},
	author = {Langue, Eva},
	year = {2008}
}

@article{noauthor_delabriere_2008,
	title = {delabriere},
	year = {2008}
}

@article{noauthor_capplin_nodate,
	title = {capplin}
}

@article{blake_proton-transfer_2009,
	title = {Proton-{Transfer} {Reaction} {Mass} {Spectrometry}},
	volume = {109},
	issn = {0009-2665, 1520-6890},
	url = {https://pubs.acs.org/doi/10.1021/cr800364q},
	doi = {10.1021/cr800364q},
	language = {en},
	number = {3},
	urldate = {2019-12-13},
	journal = {Chemical Reviews},
	author = {Blake, Robert S. and Monks, Paul S. and Ellis, Andrew M.},
	month = mar,
	year = {2009},
	pages = {861--896},
	file = {Blake et al. - 2009 - Proton-Transfer Reaction Mass Spectrometry.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\HFJWGRMU\\Blake et al. - 2009 - Proton-Transfer Reaction Mass Spectrometry.pdf:application/pdf}
}

@article{delabriere_profia:_2017,
	title = {{proFIA}: a data preprocessing workflow for flow injection analysis coupled to high-resolution mass spectrometry},
	volume = {33},
	issn = {1367-4803, 1460-2059},
	shorttitle = {{proFIA}},
	url = {https://academic.oup.com/bioinformatics/article/33/23/3767/3965327},
	doi = {10.1093/bioinformatics/btx458},
	abstract = {Motivation: Flow Injection Analysis coupled to High-Resolution Mass Spectrometry (FIA-HRMS) is a promising approach for high-throughput metabolomics. FIA-HRMS data, however, cannot be preprocessed with current software tools which rely on liquid chromatography separation, or handle low resolution data only.},
	language = {en},
	number = {23},
	urldate = {2019-12-13},
	journal = {Bioinformatics},
	author = {Delabrière, Alexis and Hohenester, Ulli M and Colsch, Benoit and Junot, Christophe and Fenaille, François and Thévenot, Etienne A},
	editor = {Stegle, Oliver},
	month = dec,
	year = {2017},
	pages = {3767--3775},
	file = {Delabrière et al. - 2017 - proFIA a data preprocessing workflow for flow inj.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\Z3P9TYAS\\Delabrière et al. - 2017 - proFIA a data preprocessing workflow for flow inj.pdf:application/pdf}
}

@article{cappellin_ptr-tof-ms_2012-1,
	title = {{PTR}-{ToF}-{MS} and data mining methods: a new tool for fruit metabolomics},
	volume = {8},
	issn = {1573-3882, 1573-3890},
	shorttitle = {{PTR}-{ToF}-{MS} and data mining methods},
	url = {http://link.springer.com/10.1007/s11306-012-0405-9},
	doi = {10.1007/s11306-012-0405-9},
	language = {en},
	number = {5},
	urldate = {2019-01-31},
	journal = {Metabolomics},
	author = {Cappellin, Luca and Soukoulis, Christos and Aprea, Eugenio and Granitto, Pablo and Dallabetta, Nicola and Costa, Fabrizio and Viola, Roberto and Märk, Tilmann D. and Gasperi, Flavia and Biasioli, Franco},
	month = oct,
	year = {2012},
	pages = {761--770},
	file = {Cappellin et al. - 2012 - PTR-ToF-MS and data mining methods a new tool for.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\785GRBMI\\Cappellin et al. - 2012 - PTR-ToF-MS and data mining methods a new tool for.pdf:application/pdf}
}

@article{devillier_metabolomics_2017-1,
	title = {Metabolomics in the {Diagnosis} and {Pharmacotherapy} of {Lung} {Diseases}},
	volume = {23},
	issn = {13816128},
	url = {http://www.eurekaselect.com/149636/article},
	doi = {10.2174/1381612823666170130155627},
	abstract = {Metabolomics is of the increasing interests in medical research and the study of respiratory diseases. This novel type of small molecule analysis can be performed not only on conventional biological samples such as plasma or urine but also on sputum, bronchoalveolar fluid, exhaled breath condensate or exhaled breath itself (which is particularly relevant for research on respiratory diseases). On one hand, powerful analytical methodologies (including mass spectrometry and nuclear magnetic resonance spectroscopy) are labour-intensive but enable the exhaustive identification of metabolites. On the other hand, electronic noses can be used for exhaled breath analysis. Although the latter devices do not contain metabolite-specific sensors, they produce a condition- or treatment-specific “breathprint” based on pattern recognition. Breath analysis with electronic noses is noninvasive, and can be performed at the bedside in real time. Here, we review the literature on metabolomics studies in respiratory medicine, with a focus on the evaluation of responses to pharmacotherapy.},
	language = {en},
	number = {14},
	urldate = {2019-03-22},
	journal = {Current Pharmaceutical Design},
	author = {Devillier, Philippe and Salvator, Helene and Naline, Emmanuel and Couderc, Louis-Jean and Grassin-Delyle, Stanislas},
	month = may,
	year = {2017},
	file = {Devillier et al. - 2017 - Metabolomics in the Diagnosis and Pharmacotherapy .pdf:C\:\\Users\\CR258086\\Zotero\\storage\\9ER6DTDD\\Devillier et al. - 2017 - Metabolomics in the Diagnosis and Pharmacotherapy .pdf:application/pdf}
}

@article{de_lacy_costello_review_2014-1,
	title = {A review of the volatiles from the healthy human body},
	volume = {8},
	issn = {1752-7155, 1752-7163},
	url = {http://stacks.iop.org/1752-7163/8/i=1/a=014001?key=crossref.b6b6a6911efb2c74c533c2e3a6bae189},
	doi = {10.1088/1752-7155/8/1/014001},
	abstract = {A compendium of all the volatile organic compounds (VOCs) emanating from the human body (the volatolome) is for the ﬁrst time reported. 1840 VOCs have been assigned from breath (872), saliva (359), blood (154), milk (256), skin secretions (532) urine (279), and faeces (381) in apparently healthy individuals. Compounds were assigned CAS registry numbers and named according to a common convention where possible. The compounds have been grouped into tables according to their chemical class or functionality to permit easy comparison. Some clear differences are observed, for instance, a lack of esters in urine with a high number in faeces. Careful use of the database is needed. The numbers may not be a true reﬂection of the actual VOCs present from each bodily excretion. The lack of a compound could be due to the techniques used or reﬂect the intensity of effort e.g. there are few publications on VOCs from blood compared to a large number on VOCs in breath. The large number of volatiles reported from skin is partly due to the methodologies used, e.g. collecting excretions on glass beads and then heating to desorb VOCs. All compounds have been included as reported (unless there was a clear discrepancy between name and chemical structure), but there may be some mistaken assignations arising from the original publications, particularly for isomers. It is the authors’ intention that this database will not only be a useful database of VOCs listed in the literature, but will stimulate further study of VOCs from healthy individuals. Establishing a list of volatiles emanating from healthy individuals and increased understanding of VOC metabolic pathways is an important step for differentiating between diseases using VOCs.},
	language = {en},
	number = {1},
	urldate = {2019-05-10},
	journal = {Journal of Breath Research},
	author = {de Lacy Costello, B and Amann, A and Al-Kateb, H and Flynn, C and Filipiak, W and Khalid, T and Osborne, D and Ratcliffe, N M},
	month = jan,
	year = {2014},
	pages = {014001},
	file = {de Lacy Costello et al. - 2014 - A review of the volatiles from the healthy human b.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\QCWM3C6J\\de Lacy Costello et al. - 2014 - A review of the volatiles from the healthy human b.pdf:application/pdf}
}

@article{holzinger_ptrwid_2015,
	title = {{PTRwid}: {A} new widget tool for processing {PTR}-{TOF}-{MS} data},
	volume = {8},
	issn = {1867-8548},
	shorttitle = {{PTRwid}},
	url = {https://www.atmos-meas-tech.net/8/3903/2015/},
	doi = {10.5194/amt-8-3903-2015},
	abstract = {PTRwid is a fast and user friendly tool that has been developed to process data from proton-transfer-reaction time-of-ﬂight mass spectrometers (PTR-TOF-MS) that use HTOF (high-resolution time-of-ﬂight) mass spectrometers from Tofwerk AG (Switzerland). PTRwid is designed for a comprehensive evaluation of whole laboratory or ﬁeld-based studies. All processing runs autonomously, and entire laboratory or ﬁeld campaigns can, in principle, be processed with a few mouse clicks.},
	language = {en},
	number = {9},
	urldate = {2019-05-20},
	journal = {Atmospheric Measurement Techniques},
	author = {Holzinger, R.},
	month = sep,
	year = {2015},
	pages = {3903--3922},
	file = {Holzinger - 2015 - PTRwid A new widget tool for processing PTR-TOF-M.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\8TLJMCEM\\Holzinger - 2015 - PTRwid A new widget tool for processing PTR-TOF-M.pdf:application/pdf}
}

@article{muller_new_2013-2,
	title = {A new software tool for the analysis of high resolution {PTR}-{TOF} mass spectra},
	volume = {127},
	issn = {01697439},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0169743913001275},
	doi = {10.1016/j.chemolab.2013.06.011},
	abstract = {The High Resolution Proton-Transfer-Reaction Time-of-Flight Mass Spectrometer (HR PTR-TOF-MS) is a powerful analytical tool used by various scientiﬁc communities for real-time measurements of volatile organic compounds (VOC). The analysis of HR PTR-TOF-MS data is, however, particularly demanding because of the large amount of complex data being generated. Based on recently developed or described mathematical methods, we have produced a new software tool, the PTR-TOF Data Analyzer, which greatly facilitates the data analysis process. The new software solution allows for i) a combined Poisson counting statistics and dead time correction of ion count rates, ii) accurate mass axis calibration, iii) an iterative residual peak analysis that detects up to 5 isobaric peaks per unit m/z, iv) time series analysis of both low and high mass and time resolution data and v) visualization of analysis results for fast quality assurance checks. After having been successfully tested by a group of users with different application needs, the PTR-TOF Data Analyzer is made generally available to the scientiﬁc community. This will improve the user-friendliness of the PTR-TOF-MS technique and facilitate scientiﬁc work with this new analytical mass spectrometer.},
	language = {en},
	urldate = {2019-01-31},
	journal = {Chemometrics and Intelligent Laboratory Systems},
	author = {Müller, Markus and Mikoviny, Tomáš and Jud, Werner and D'Anna, Barbara and Wisthaler, Armin},
	month = aug,
	year = {2013},
	pages = {158--165},
	file = {Müller et al. - 2013 - A new software tool for the analysis of high resol.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\96CJQ9YU\\Müller et al. - 2013 - A new software tool for the analysis of high resol.pdf:application/pdf}
}

@article{clayton_snip_nodate-1,
	title = {{SNIP}, {A} {STATISTICS}-{SENSITIVE} {BACKGROUND} {TREATMENT} {FOR} {THE} {QUANTITATIVE} {ANALYSIS} {OF} {PIXE} {SPECTFtA} {IN} {GEOSCIENCE} {APPLICATIONS}},
	language = {en},
	author = {CLAYTON, C G RYAN and Clayton, E and Griffin, W L and Sie, S H},
	pages = {7},
	file = {If et al. - SNIP, A STATISTICS-SENSITIVE BACKGROUND TREATMENT .pdf:C\:\\Users\\CR258086\\Zotero\\storage\\SRUDXGWS\\If et al. - SNIP, A STATISTICS-SENSITIVE BACKGROUND TREATMENT .pdf:application/pdf}
}

@article{savitzky_smoothing_1964-2,
	title = {Smoothing and {Differentiation} of {Data} by {Simplified} {Least} {Squares} {Procedures}.},
	volume = {36},
	issn = {0003-2700, 1520-6882},
	url = {http://pubs.acs.org/doi/abs/10.1021/ac60214a047},
	doi = {10.1021/ac60214a047},
	language = {en},
	number = {8},
	urldate = {2019-03-05},
	journal = {Analytical Chemistry},
	author = {Savitzky, Abraham. and Golay, M. J. E.},
	month = jul,
	year = {1964},
	pages = {1627--1639},
	file = {Savitzky et Golay - 1964 - Smoothing and Differentiation of Data by Simplifie.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\J3KCNTS2\\Savitzky et Golay - 1964 - Smoothing and Differentiation of Data by Simplifie.pdf:application/pdf}
}

@article{vivo-truyols_automatic_2006-2,
	title = {Automatic {Selection} of {Optimal} {Savitzky}−{Golay} {Smoothing}},
	volume = {78},
	issn = {0003-2700, 1520-6882},
	url = {https://pubs.acs.org/doi/10.1021/ac0600196},
	doi = {10.1021/ac0600196},
	language = {en},
	number = {13},
	urldate = {2019-03-06},
	journal = {Analytical Chemistry},
	author = {Vivó-Truyols, Gabriel and Schoenmakers, Peter J.},
	month = jul,
	year = {2006},
	pages = {4598--4608},
	file = {Vivó-Truyols et Schoenmakers - 2006 - Automatic Selection of Optimal Savitzky−Golay Smoo.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\5PD3VDW8\\Vivó-Truyols et Schoenmakers - 2006 - Automatic Selection of Optimal Savitzky−Golay Smoo.pdf:application/pdf}
}

@article{langue_analysis_2008-1,
	title = {Analysis of mass spectrometric data: peak picking and map alignment},
	author = {Langue, Eva},
	year = {2008}
}

@article{blake_proton-transfer_2009-1,
	title = {Proton-{Transfer} {Reaction} {Mass} {Spectrometry}},
	volume = {109},
	issn = {0009-2665, 1520-6890},
	url = {https://pubs.acs.org/doi/10.1021/cr800364q},
	doi = {10.1021/cr800364q},
	language = {en},
	number = {3},
	urldate = {2019-12-13},
	journal = {Chemical Reviews},
	author = {Blake, Robert S. and Monks, Paul S. and Ellis, Andrew M.},
	month = mar,
	year = {2009},
	pages = {861--896},
	file = {Blake et al. - 2009 - Proton-Transfer Reaction Mass Spectrometry.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\BDITCMPQ\\Blake et al. - 2009 - Proton-Transfer Reaction Mass Spectrometry.pdf:application/pdf}
}

@article{delabriere_profia_2017,
	title = {{proFIA}: a data preprocessing workflow for flow injection analysis coupled to high-resolution mass spectrometry},
	volume = {33},
	issn = {1367-4803, 1460-2059},
	shorttitle = {{proFIA}},
	url = {https://academic.oup.com/bioinformatics/article/33/23/3767/3965327},
	doi = {10.1093/bioinformatics/btx458},
	abstract = {Motivation: Flow Injection Analysis coupled to High-Resolution Mass Spectrometry (FIA-HRMS) is a promising approach for high-throughput metabolomics. FIA-HRMS data, however, cannot be preprocessed with current software tools which rely on liquid chromatography separation, or handle low resolution data only.},
	language = {en},
	number = {23},
	urldate = {2019-12-13},
	journal = {Bioinformatics},
	author = {Delabrière, Alexis and Hohenester, Ulli M and Colsch, Benoit and Junot, Christophe and Fenaille, François and Thévenot, Etienne A},
	editor = {Stegle, Oliver},
	month = dec,
	year = {2017},
	pages = {3767--3775},
	file = {Delabrière et al. - 2017 - proFIA a data preprocessing workflow for flow inj.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\M9UPVNEE\\Delabrière et al. - 2017 - proFIA a data preprocessing workflow for flow inj.pdf:application/pdf}
}

@article{brown_design_1991,
	title = {Design and performance of a matrix-assisted laser desorption time-of-flight mass spectrometer utilizing a pulsed nitrogen laser},
	volume = {248},
	issn = {00032670},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0003267000846735},
	doi = {10.1016/S0003-2670(00)84673-5},
	abstract = {The design conslderatlons and expenmental performance of a lmear time-of-fhght mass spectrometer are reported for performmg matnx-assisted laser desorptlon studies A simple pulsed gas-discharge nitrogen laser (337.1 nm) 1s successfully used m contrast to the more widely used frequency-quadrupled (266 nm) or frequency-tnpled (355 nm) Nd YAG sold-state laser Optical considerations m utkmg the puked mtrogen laser are \&cussed and a simple optlcal arrangement 1s described which allows for sultable imagmg of the poor spatial beam profile of the pulsed mtrogen laser Laser spot sues of 150 X 450 pm are obtainable As with the frequency-tnpled Nd : YAG laser, smapimc acid is found to be the most useful matnx for producing protonated molecular species from proteins. Appropnate laser power levels are determmcd, as are matnx/sample levels. Adequate response for most small to medmm molecular weight protems is obtamed for less than 1 pmol of sample. A simple emsel lens Incorporated into the ion source does not appear to provide any slgmficant focusing of the laser-desorbed ions, however, a constant d.c. voltage apphed to beam steenng pIates enhances the ion signal slgmflcantIy Selective, puked denectlon of the low-mass tons produced from the matrix 1s also utdized to prevent excessive saturation of the microchannel plate ion detector. High source potentials are found to provide improved resolution and sensitlvlty in comparison mth lower source potentials combined {\textasciitilde}th post-acceleration at the detector Representative mass spectra of several proteins and peptides are presented Increased formation of photoinduced adduct ions are observed m comparison with that reported for matrix-assisted laser desorption expenments utlhzmg a Nd YAG laser and significant amounts of dlmer and tnmer Ions are produced. The former may be due to non-optmuzed sample/matnx composmons as opposed to wavelength-induced effects, whereas the latter 1s only observed at higher protein concentrations. Slgmflcantly more peak broademng than would normally be expected IS observed above 20000 u This may be due to the post-acceleration design of the rmcrochannel plate detector used.},
	language = {en},
	number = {2},
	urldate = {2020-01-15},
	journal = {Analytica Chimica Acta},
	author = {Brown, R.S. and Gilfrich, N.L.},
	month = aug,
	year = {1991},
	pages = {541--552},
	file = {Brown et Gilfrich - 1991 - Design and performance of a matrix-assisted laser .pdf:C\:\\Users\\CR258086\\Zotero\\storage\\PZZ5QN7G\\Brown et Gilfrich - 1991 - Design and performance of a matrix-assisted laser .pdf:application/pdf}
}

@article{holzinger_chemical_2013,
	title = {Chemical evolution of organic aerosol in {Los} {Angeles} during the {CalNex} 2010 study},
	volume = {13},
	issn = {1680-7324},
	url = {https://www.atmos-chem-phys.net/13/10125/2013/},
	doi = {10.5194/acp-13-10125-2013},
	abstract = {Abstract. During the CalNex study (15 May to 16 June 2010) a large suite of instruments was operated at the Los Angeles area ground supersite to characterize the sources and atmospheric processing of atmospheric pollution. The thermal-desorption proton-transfer-reaction mass-spectrometer (TD-PTR-MS) was deployed to an urban area for the first time and detected 691 organic ions in aerosol samples, the mean total concentration of which was estimated as 3.3 μg m−3. Based on comparison to total organic aerosol (OA) measurements, we estimate that approximately 50\% of the OA mass at this site was directly measured by the TD-PTR-MS. Based on correlations with aerosol mass spectrometer (AMS) OA components, the ions were grouped to represent hydrocarbon-like OA (HOA), local OA (LOA), semi-volatile oxygenated OA (SV-OOA), and low volatility oxygenated OA (LV-OOA). Mass spectra and thermograms of the ion groups are mostly consistent with the assumed sources and/or photochemical origin of the OA components. The mass spectra of ions representing the primary components HOA and LOA included the highest m/z, consistent with their higher resistance to thermal decomposition, and they were volatilized at lower temperatures ({\textasciitilde} 150 °C). Photochemical ageing weakens C-C bond strengths (also resulting in chemical fragmentation), and produces species of lower volatility (through the addition of functional groups). Accordingly the mass spectra of ions representing the oxidized OA components (SV-OOA, and LV-OOA) lack the highest masses and they are volatilized at higher temperatures (250–300 °C). Chemical parameters like mean carbon number (nC), mean carbon oxidation state (OSC), and the atomic ratios O / C and H / C of the ion groups are consistent with the expected sources and photochemical processing of the aerosol components. Our data suggest that chemical fragmentation gains importance over functionalization as photochemical age of OA increases. Surprisingly, the photochemical age of OA decreases during the daytime hours, demonstrating the importance of rapid production of new (photochemically young) SV-OOA during daytime. The PTR detects higher organic N concentrations than the AMS, the reasons for which are not well understood and cannot be explained by known artifacts related to PTR or the AMS. The median atomic N / C ratio (6.4\%) of the ion group representing LV-OOA is a factor 2 higher than N / C of any other ion group. This suggests a multiphase chemical source involving ammonium ions is contributing to LV-OOA.},
	language = {en},
	number = {19},
	urldate = {2020-01-22},
	journal = {Atmospheric Chemistry and Physics},
	author = {Holzinger, R. and Goldstein, A. H. and Hayes, P. L. and Jimenez, J. L. and Timkovsky, J.},
	month = oct,
	year = {2013},
	pages = {10125--10141},
	file = {Holzinger et al. - 2013 - Chemical evolution of organic aerosol in Los Angel.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\8V6MQJVD\\Holzinger et al. - 2013 - Chemical evolution of organic aerosol in Los Angel.pdf:application/pdf}
}

@article{kuo_human_2020,
	title = {Human {Breathomics} {Database}},
	volume = {2020},
	language = {en},
	author = {Kuo, Tien-Chueh and Tan, Cheng-En and Wang, San-Yuan and Lin, Olivia A and Su, Bo-Han and Hsu, Ming-Tsung and Lin, Jessica and Cheng, Yu-Yen and Chen, Ciao-Sin and Yang, Yu-Chieh and Chen, Kuo-Hsing and Lin, Shu-Wen and Ho, Chao-Chi and Kuo, Ching-Hua and Tseng, Yufeng Jane},
	year = {2020},
	pages = {8},
	file = {Kuo et al. - 2020 - Human Breathomics Database.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\5EZUFG3Q\\Kuo et al. - 2020 - Human Breathomics Database.pdf:application/pdf}
}

@article{vita_tuberomics_2020,
	title = {Tuberomics: a molecular profiling for the adaption of edible fungi ({Tuber} magnatum {Pico}) to different natural environments},
	volume = {21},
	issn = {1471-2164},
	shorttitle = {Tuberomics},
	url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6522-3},
	doi = {10.1186/s12864-020-6522-3},
	abstract = {Background: Truffles are symbiotic fungi that develop underground in association with plant roots, forming ectomycorrhizae. They are primarily known for the organoleptic qualities of their hypogeous fruiting bodies. Primarily, Tuber magnatum Pico is a greatly appreciated truffle species mainly distributed in Italy and Balkans. Its price and features are mostly depending on its geographical origin. However, the genetic variation within T. magnatum has been only partially investigated as well as its adaptation to several environments.
Results: Here, we applied an integrated omic strategy to T. magnatum fruiting bodies collected during several seasons from three different areas located in the North, Center and South of Italy, with the aim to distinguish them according to molecular and biochemical traits and to verify the impact of several environments on these properties. With the proteomic approach based on two-dimensional electrophoresis (2-DE) followed by mass spectrometry, we were able to identify proteins specifically linked to the sample origin. We further associated the proteomic results to an RNA-seq profiling, which confirmed the possibility to differentiate samples according to their source and provided a basis for the detailed analysis of genes involved in sulfur metabolism. Finally, geographical specificities were associated with the set of volatile compounds produced by the fruiting bodies, as quantitatively and qualitatively determined through proton transfer reaction-mass spectrometry (PTR-MS) and gas-chromatographymass spectrometry (GC-MS). In particular, a partial least squares-discriminant analysis (PLS-DA) model built from the latter data was able to return high confidence predictions of sample source.
Conclusions: Results provide a characterization of white fruiting bodies by a wide range of different molecules, suggesting the role for specific compounds in the responses and adaptation to distinct environments.},
	language = {en},
	number = {1},
	urldate = {2020-02-04},
	journal = {BMC Genomics},
	author = {Vita, Federico and Giuntoli, Beatrice and Bertolini, Edoardo and Taiti, Cosimo and Marone, Elettra and D’Ambrosio, Chiara and Trovato, Emanuela and Sciarrone, Danilo and Zoccali, Mariosimone and Balestrini, Raffaella and Scaloni, Andrea and Mondello, Luigi and Mancuso, Stefano and Alessio, Massimo and Alpi, Amedeo},
	month = dec,
	year = {2020},
	pages = {90},
	file = {Vita et al. - 2020 - Tuberomics a molecular profiling for the adaption.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\ZRH6UTTQ\\Vita et al. - 2020 - Tuberomics a molecular profiling for the adaption.pdf:application/pdf}
}

@article{treutler_prediction_2016,
	title = {Prediction, {Detection}, and {Validation} of {Isotope} {Clusters} in {Mass} {Spectrometry} {Data}},
	volume = {6},
	issn = {2218-1989},
	url = {http://www.mdpi.com/2218-1989/6/4/37},
	doi = {10.3390/metabo6040037},
	abstract = {Mass spectrometry is a key analytical platform for metabolomics. The precise quantiﬁcation and identiﬁcation of small molecules is a prerequisite for elucidating the metabolism and the detection, validation, and evaluation of isotope clusters in LC-MS data is important for this task. Here, we present an approach for the improved detection of isotope clusters using chemical prior knowledge and the validation of detected isotope clusters depending on the substance mass using database statistics. We ﬁnd remarkable improvements regarding the number of detected isotope clusters and are able to predict the correct molecular formula in the top three ranks in 92\% of the cases. We make our methodology freely available as part of the Bioconductor packages xcms version 1.50.0 and CAMERA version 1.30.0.},
	language = {en},
	number = {4},
	urldate = {2020-02-04},
	journal = {Metabolites},
	author = {Treutler, Hendrik and Neumann, Steffen},
	month = oct,
	year = {2016},
	pages = {37},
	file = {Treutler et Neumann - 2016 - Prediction, Detection, and Validation of Isotope C.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\HBL8UQFX\\Treutler et Neumann - 2016 - Prediction, Detection, and Validation of Isotope C.pdf:application/pdf}
}

@article{smith_xcms_2006,
	title = {{XCMS}: {Processing} {Mass} {Spectrometry} {Data} for {Metabolite} {Profiling} {Using} {Nonlinear} {Peak} {Alignment}, {Matching}, and {Identification}},
	volume = {78},
	issn = {0003-2700, 1520-6882},
	shorttitle = {{XCMS}},
	url = {https://pubs.acs.org/doi/10.1021/ac051437y},
	doi = {10.1021/ac051437y},
	language = {en},
	number = {3},
	urldate = {2020-02-05},
	journal = {Analytical Chemistry},
	author = {Smith, Colin A. and Want, Elizabeth J. and O'Maille, Grace and Abagyan, Ruben and Siuzdak, Gary},
	month = feb,
	year = {2006},
	pages = {779--787},
	file = {Smith et al. - 2006 - XCMS Processing Mass Spectrometry Data for Metabo.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\K9R8BAJ8\\Smith et al. - 2006 - XCMS Processing Mass Spectrometry Data for Metabo.pdf:application/pdf}
}

@article{pluskal_mzmine_2010,
	title = {{MZmine} 2: {Modular} framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data},
	volume = {11},
	issn = {1471-2105},
	shorttitle = {{MZmine} 2},
	url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-395},
	doi = {10.1186/1471-2105-11-395},
	abstract = {Background: Mass spectrometry (MS) coupled with online separation methods is commonly applied for differential and quantitative profiling of biological samples in metabolomic as well as proteomic research. Such approaches are used for systems biology, functional genomics, and biomarker discovery, among others. An ongoing challenge of these molecular profiling approaches, however, is the development of better data processing methods. Here we introduce a new generation of a popular open-source data processing toolbox, MZmine 2.
Results: A key concept of the MZmine 2 software design is the strict separation of core functionality and data processing modules, with emphasis on easy usability and support for high-resolution spectra processing. Data processing modules take advantage of embedded visualization tools, allowing for immediate previews of parameter settings. Newly introduced functionality includes the identification of peaks using online databases, MSn data support, improved isotope pattern support, scatter plot visualization, and a new method for peak list alignment based on the random sample consensus (RANSAC) algorithm. The performance of the RANSAC alignment was evaluated using synthetic datasets as well as actual experimental data, and the results were compared to those obtained using other alignment algorithms.
Conclusions: MZmine 2 is freely available under a GNU GPL license and can be obtained from the project website at: http://mzmine.sourceforge.net/. The current version of MZmine 2 is suitable for processing large batches of data and has been applied to both targeted and non-targeted metabolomic analyses.},
	language = {en},
	number = {1},
	urldate = {2020-02-05},
	journal = {BMC Bioinformatics},
	author = {Pluskal, Tomáš and Castillo, Sandra and Villar-Briones, Alejandro and Orešič, Matej},
	month = dec,
	year = {2010},
	pages = {395},
	file = {Pluskal et al. - 2010 - MZmine 2 Modular framework for processing, visual.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\AC22R8Y2\\Pluskal et al. - 2010 - MZmine 2 Modular framework for processing, visual.pdf:application/pdf}
}

@article{katajamaa_mzmine_2006,
	title = {{MZmine}: toolbox for processing and visualization of mass spectrometry based molecular profile data},
	volume = {22},
	issn = {1367-4803, 1460-2059},
	shorttitle = {{MZmine}},
	url = {https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btk039},
	doi = {10.1093/bioinformatics/btk039},
	abstract = {Summary: New additional methods are presented for processing and visualizing mass spectrometry based molecular profile data, implemented as part of the recently introduced MZmine software. They include new features and extensions such as support for mzXML data format, capability to perform batch processing for large number of files, support for parallel processing, new methods for calculating peak areas using post-alignment peak picking algorithm and implementation of Sammon’s mapping and curvilinear distance analysis for data visualization and exploratory analysis.},
	language = {en},
	number = {5},
	urldate = {2020-02-05},
	journal = {Bioinformatics},
	author = {Katajamaa, M. and Miettinen, J. and Oresic, M.},
	month = mar,
	year = {2006},
	pages = {634--636},
	file = {Katajamaa et al. - 2006 - MZmine toolbox for processing and visualization o.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\3R2QMZHH\\Katajamaa et al. - 2006 - MZmine toolbox for processing and visualization o.pdf:application/pdf}
}

@article{delabriere_profia_2017-1,
	title = {{proFIA}: a data preprocessing workflow for flow injection analysis coupled to high-resolution mass spectrometry},
	volume = {33},
	issn = {1367-4803, 1460-2059},
	shorttitle = {{proFIA}},
	url = {https://academic.oup.com/bioinformatics/article/33/23/3767/3965327},
	doi = {10.1093/bioinformatics/btx458},
	abstract = {Motivation: Flow Injection Analysis coupled to High-Resolution Mass Spectrometry (FIA-HRMS) is a promising approach for high-throughput metabolomics. FIA-HRMS data, however, cannot be preprocessed with current software tools which rely on liquid chromatography separation, or handle low resolution data only.},
	language = {en},
	number = {23},
	urldate = {2020-02-05},
	journal = {Bioinformatics},
	author = {Delabrière, Alexis and Hohenester, Ulli M and Colsch, Benoit and Junot, Christophe and Fenaille, François and Thévenot, Etienne A},
	editor = {Stegle, Oliver},
	month = dec,
	year = {2017},
	pages = {3767--3775},
	file = {Delabrière et al. - 2017 - proFIA a data preprocessing workflow for flow inj.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\N7TF2WDC\\Delabrière et al. - 2017 - proFIA a data preprocessing workflow for flow inj.pdf:application/pdf}
}

@article{moser_mass_2005,
	title = {Mass spectrometric profile of exhaled breath—field study by {PTR}-{MS}},
	volume = {145},
	issn = {15699048},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1569904804000266},
	doi = {10.1016/j.resp.2004.02.002},
	abstract = {Recently, increased interest has focused on the diagnostic potential of volatile organic compounds (VOC) exhaled in human breath as this substance group has been conjectured in indoor air quality and disease screening. Proton transfer reaction-mass spectrometry (PTR-MS) has been established as a new tool for a rapid determination of exhaled air proﬁle. However, no investigations have been carried out into the proﬁle of exhaled air as determined by PTR-MS. Therefore, it was the aim of the present study to determine the proﬁle of exhaled breath in a ﬁeld survey enrolling 344 persons. Analysis was performed using PTR-MS. No signiﬁcant correlations with age, blood pressure, and body mass index could be observed with any molecular mass. The present study delineates possible reference values for PTR-MS investigations into exhaled air proﬁle. In conclusion, the present study was the ﬁrst to delineate mass spectrometric characteristics of an average patient sample as possible reference values.},
	language = {en},
	number = {2-3},
	urldate = {2020-02-10},
	journal = {Respiratory Physiology \& Neurobiology},
	author = {Moser, Berthold and Bodrogi, Florian and Eibl, Guenther and Lechner, Matthias and Rieder, Josef and Lirk, Philipp},
	month = feb,
	year = {2005},
	pages = {295--300},
	file = {Moser et al. - 2005 - Mass spectrometric profile of exhaled breath—field.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\JSQQ2W5V\\Moser et al. - 2005 - Mass spectrometric profile of exhaled breath—field.pdf:application/pdf}
}

@article{bocker_sirius_2009,
	title = {{SIRIUS}: decomposing isotope patterns for metabolite identification†},
	volume = {25},
	issn = {1460-2059, 1367-4803},
	shorttitle = {{SIRIUS}},
	url = {https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btn603},
	doi = {10.1093/bioinformatics/btn603},
	abstract = {Motivation: High-resolution mass spectrometry (MS) is among the most widely used technologies in metabolomics. Metabolites participate in almost all cellular processes, but most metabolites still remain uncharacterized. Determination of the sum formula is a crucial step in the identiﬁcation of an unknown metabolite, as it reduces its possible structures to a hopefully manageable set.},
	language = {en},
	number = {2},
	urldate = {2020-02-10},
	journal = {Bioinformatics},
	author = {Böcker, Sebastian and Letzel, Matthias C. and Lipták, Zsuzsanna and Pervukhin, Anton},
	month = jan,
	year = {2009},
	pages = {218--224},
	file = {Böcker et al. - 2009 - SIRIUS decomposing isotope patterns for metabolit.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\RAJWRBQ4\\Böcker et al. - 2009 - SIRIUS decomposing isotope patterns for metabolit.pdf:application/pdf}
}

@article{kuhl_lc-ms_nodate,
	title = {{LC}-{MS} {Peak} {Annotation} and {Identiﬁcation} with {CAMERA}},
	language = {en},
	author = {Kuhl, Carsten and Tautenhahn, Ralf and Neumann, Steﬀen},
	pages = {15},
	file = {Kuhl et al. - LC-MS Peak Annotation and Identiﬁcation with CAMER.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\AB5LPQMU\\Kuhl et al. - LC-MS Peak Annotation and Identiﬁcation with CAMER.pdf:application/pdf}
}

@article{trefz_continuous_2013,
	title = {Continuous {Real} {Time} {Breath} {Gas} {Monitoring} in the {Clinical} {Environment} by {Proton}-{Transfer}-{Reaction}-{Time}-of-{Flight}-{Mass} {Spectrometry}},
	volume = {85},
	issn = {0003-2700, 1520-6882},
	url = {https://pubs.acs.org/doi/10.1021/ac402298v},
	doi = {10.1021/ac402298v},
	abstract = {Analysis of volatile organic compounds (VOCs) in breath holds great promise for noninvasive diagnostic applications. However, concentrations of VOCs in breath may change quickly, and actual and previous uptakes of exogenous substances, especially in the clinical environment, represent crucial issues. We therefore adapted proton-transfer-reaction-time-of-ﬂight-mass spectrometry for real time breath analysis in the clinical environment. For reasons of medical safety, a 6 m long heated silcosteel transfer line connected to a sterile mouth piece was used for breath sampling from spontaneously breathing volunteers and mechanically ventilated patients. A time resolution of 200 ms was applied. Breath from mechanically ventilated patients was analyzed immediately after cardiac surgery. Breath from 32 members of staﬀ was analyzed in the post anesthetic care unit (PACU). In parallel, room air was measured continuously over 7 days. Detection limits for breath-resolved real time measurements were in the high pptV/low ppbV range. Assignment of signals to alveolar or inspiratory phases was done automatically by a matlab-based algorithm. Quickly and abruptly occurring changes of patients’ clinical status could be monitored in terms of breath-to-breath variations of VOC (e.g. isoprene) concentrations. In the PACU, room air concentrations mirrored occupancy. Exhaled concentrations of sevoﬂurane strongly depended on background concentrations in all participants. In combination with an optimized inlet system, the high time and mass resolution of PTR-ToF-MS provides optimal conditions to trace quick changes of breath VOC proﬁles and to assess eﬀects from the clinical environment.},
	language = {en},
	number = {21},
	urldate = {2020-02-12},
	journal = {Analytical Chemistry},
	author = {Trefz, Phillip and Schmidt, Markus and Oertel, Peter and Obermeier, Juliane and Brock, Beate and Kamysek, Svend and Dunkl, Jürgen and Zimmermann, Ralf and Schubert, Jochen K. and Miekisch, Wolfram},
	month = nov,
	year = {2013},
	pages = {10321--10329},
	file = {Trefz et al. - 2013 - Continuous Real Time Breath Gas Monitoring in the .pdf:C\:\\Users\\CR258086\\Zotero\\storage\\BIEVVY7V\\Trefz et al. - 2013 - Continuous Real Time Breath Gas Monitoring in the .pdf:application/pdf}
}

@article{muller_detector_2014-1,
	title = {Detector aging induced mass discrimination and non-linearity effects in {PTR}-{ToF}-{MS}},
	volume = {365-366},
	issn = {13873806},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1387380613004338},
	doi = {10.1016/j.ijms.2013.12.008},
	abstract = {In this short technical paper we demonstrate how aging of the micro-channel plate (MCP) detector in a PTR-ToF-MS instrument induces strong mass discrimination and detection non-linearity effects. Based on exemplary data from an 11-week measurement campaign we show how detector aging led to an m/zdependent loss in detection efﬁciency in the m/z 33 (−19\%) to m/z 205 range (−67\%). Ion signals in the upper m/z range did not increase linearly with analyte concentration (0–150 ppbv) when the MCP detector was not operated in the saturation regime. Both effects may lead to large errors in VOC quantiﬁcation by PTR-ToF-MS if the instrument is not externally calibrated on a frequent basis. We also demonstrate that the current practice of minimizing ion feedback in the MCP detector will trigger the described problems. Our study may serve as a guide for diagnosing and optimizing PTR-ToF-MS detector performance.},
	language = {en},
	urldate = {2020-03-03},
	journal = {International Journal of Mass Spectrometry},
	author = {Müller, M. and Mikoviny, T. and Wisthaler, A.},
	month = may,
	year = {2014},
	pages = {93--97},
	file = {Müller et al. - 2014 - Detector aging induced mass discrimination and non.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\EQWYMMR7\\Müller et al. - 2014 - Detector aging induced mass discrimination and non.pdf:application/pdf}
}

@article{blake_demonstration_2004,
	title = {Demonstration of {Proton}-{Transfer} {Reaction} {Time}-of-{Flight} {Mass} {Spectrometry} for {Real}-{Time} {Analysis} of {Trace} {Volatile} {Organic} {Compounds}},
	volume = {76},
	issn = {0003-2700, 1520-6882},
	url = {https://pubs.acs.org/doi/10.1021/ac0498260},
	doi = {10.1021/ac0498260},
	language = {en},
	number = {13},
	urldate = {2020-03-03},
	journal = {Analytical Chemistry},
	author = {Blake, Robert S. and Whyte, Christopher and Hughes, Ceri O. and Ellis, Andrew M. and Monks, Paul S.},
	month = jul,
	year = {2004},
	pages = {3841--3845},
	file = {Blake et al. - 2004 - Demonstration of Proton-Transfer Reaction Time-of-.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\NTYF4LQ5\\Blake et al. - 2004 - Demonstration of Proton-Transfer Reaction Time-of-.pdf:application/pdf}
}

@article{stavropoulos_implementation_2020,
	title = {Implementation of quality controls is essential to prevent batch effects in breathomics data and allow for cross-study comparisons},
	issn = {1752-7155, 1752-7163},
	url = {https://iopscience.iop.org/article/10.1088/1752-7163/ab7b8d},
	doi = {10.1088/1752-7163/ab7b8d},
	language = {en},
	urldate = {2020-03-04},
	journal = {Journal of Breath Research},
	author = {Stavropoulos, Georgios and Jonkers, Daisy M A E and Mujagic, Zlatan and Koek, Ger H and Masclee, Ad A M and Pierik, Marieke J and Dallinga, Jan and van Schooten, Frederik Jan and Smolinska, Agnieszka},
	month = mar,
	year = {2020},
	file = {Stavropoulos et al. - 2020 - Implementation of quality controls is essential to.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\2AJZGUMU\\Stavropoulos et al. - 2020 - Implementation of quality controls is essential to.pdf:application/pdf}
}

@article{blake_demonstration_2004-1,
	title = {Demonstration of {Proton}-{Transfer} {Reaction} {Time}-of-{Flight} {Mass} {Spectrometry} for {Real}-{Time} {Analysis} of {Trace} {Volatile} {Organic} {Compounds}},
	volume = {76},
	issn = {0003-2700, 1520-6882},
	url = {https://pubs.acs.org/doi/10.1021/ac0498260},
	doi = {10.1021/ac0498260},
	language = {en},
	number = {13},
	urldate = {2020-03-04},
	journal = {Analytical Chemistry},
	author = {Blake, Robert S. and Whyte, Christopher and Hughes, Ceri O. and Ellis, Andrew M. and Monks, Paul S.},
	month = jul,
	year = {2004},
	pages = {3841--3845},
	file = {Blake et al. - 2004 - Demonstration of Proton-Transfer Reaction Time-of-.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\CG6QS5KN\\Blake et al. - 2004 - Demonstration of Proton-Transfer Reaction Time-of-.pdf:application/pdf}
}

@article{fischer_non-isobaric_2018,
	title = {Non-isobaric time-of-flight correction for isobar resolving in {MR}-{ToF} mass spectrometry},
	volume = {432},
	issn = {13873806},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1387380618301507},
	doi = {10.1016/j.ijms.2018.07.004},
	abstract = {A development in multi-reﬂection time-of-ﬂight (MR-ToF) mass spectrometry is presented with which isobars are resolved by means of an ofﬂine correction with the signal of a non-isobaric ion species. The method is demonstrated for a pair of Cr2+ isobars with a relative mass difference of 1.8 · 10−5, with either an additional, non-isobaric Cr+2 or a CrO+ ion appearing in the same time-of-ﬂight spectrum, although at a different number of revolutions during the same storage time. This is in contrast to earlier applications where ToF shift corrections are performed with ions at identical revolution numbers, typically isobars that are also acting as mass-reference ions. It is shown that ions of virtually any mass simultaneously stored in the MR-ToF analyzer can be employed. This is particularly useful in situations where both the ions of interest and the reference ions for mass calibration have only small count rates not sufﬁcient for the ToF-shift corrections. For the present system, the resolving power increases by more than a factor of two when the ofﬂine drift correction is applied.},
	language = {en},
	urldate = {2020-03-04},
	journal = {International Journal of Mass Spectrometry},
	author = {Fischer, Paul and Knauer, Stefan and Marx, Gerrit and Schweikhard, Lutz},
	month = sep,
	year = {2018},
	pages = {44--51},
	file = {Fischer et al. - 2018 - Non-isobaric time-of-flight correction for isobar .pdf:C\:\\Users\\CR258086\\Zotero\\storage\\DIIGYBU7\\Fischer et al. - 2018 - Non-isobaric time-of-flight correction for isobar .pdf:application/pdf}
}

@article{miekisch_impact_2008,
	title = {Impact of sampling procedures on the results of breath analysis},
	volume = {2},
	issn = {1752-7155, 1752-7163},
	url = {http://stacks.iop.org/1752-7163/2/i=2/a=026007?key=crossref.8604809836ce670fcb15d956965e8a96},
	doi = {10.1088/1752-7155/2/2/026007},
	abstract = {The impact of different sampling techniques on the results of breath analysis was to be assessed in this study. Alveolar, mixed expiratory and time-controlled samples were collected from ten volunteers and from eight lung cancer patients. Breath sampling was visually controlled by means of capnometry. PCO2 and 13 VOCs were determined. Mixed expiratory sampling yielded 25\% lower concentrations of CO2 and blood-borne VOCs. Time-controlled sampling generated high variation of results. Ratios Calv/Cmixed were {\textgreater}1.5 for CO2, acetone and isoprene, and {\textless}1 for isopropanol, 2-butanone and hexanal. Acetonitrile, butane, dimethylsulﬁde, pentane, butanal, benzene and hexane showed 1.5 {\textgreater} Calv/Cmixed {\textgreater} 1. The ratio Calv/Cmixed of CO2, acetone and isoprene was different in healthy volunteers and lung cancer patients. Alveolar samples showed the highest concentrations of endogenous and lowest concentration of exogenous substances. Sampling can impact results in breath analysis. Valuable information can be obtained from ratios of alveolar and mixed expired concentrations.},
	language = {en},
	number = {2},
	urldate = {2020-03-12},
	journal = {Journal of Breath Research},
	author = {Miekisch, Wolfram and Kischkel, Sabine and Sawacki, Annika and Liebau, Tina and Mieth, Maren and Schubert, Jochen K},
	month = jun,
	year = {2008},
	pages = {026007},
	file = {Miekisch et al. - 2008 - Impact of sampling procedures on the results of br.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\HRYJVLDZ\\Miekisch et al. - 2008 - Impact of sampling procedures on the results of br.pdf:application/pdf}
}

@article{van_den_velde_differences_2007,
	title = {Differences between {Alveolar} {Air} and {Mouth} {Air}},
	volume = {79},
	issn = {0003-2700, 1520-6882},
	url = {https://pubs.acs.org/doi/10.1021/ac062009a},
	doi = {10.1021/ac062009a},
	language = {en},
	number = {9},
	urldate = {2020-03-12},
	journal = {Analytical Chemistry},
	author = {van den Velde, Sandra and Quirynen, Marc and van Hee, Paul and van Steenberghe, Daniel},
	month = may,
	year = {2007},
	pages = {3425--3429},
	annote = {mounth air : 150 premier ml
alveolar air : 350 dernier ml
soustraction entre air expiré et air ambiant
les patient on respirer 60 min dans la salle avant de collecter l'air
no fasting volunters
jeuner influence la concentration d'acétone},
	file = {van den Velde et al. - 2007 - Differences between Alveolar Air and Mouth Air.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\7CYIGWXN\\van den Velde et al. - 2007 - Differences between Alveolar Air and Mouth Air.pdf:application/pdf}
}

@article{ghorbani_modeling_2018,
	title = {Modeling {Pulmonary} {Gas} {Exchange} and {Single}-{Exhalation} {Profiles} of {Carbon} {Monoxide}},
	volume = {9},
	issn = {1664-042X},
	url = {https://www.frontiersin.org/article/10.3389/fphys.2018.00927/full},
	doi = {10.3389/fphys.2018.00927},
	language = {en},
	urldate = {2020-03-12},
	journal = {Frontiers in Physiology},
	author = {Ghorbani, Ramin and Blomberg, Anders and Schmidt, Florian M.},
	month = jul,
	year = {2018},
	pages = {927},
	file = {Ghorbani et al. - 2018 - Modeling Pulmonary Gas Exchange and Single-Exhalat.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\3TI2QFMQ\\Ghorbani et al. - 2018 - Modeling Pulmonary Gas Exchange and Single-Exhalat.pdf:application/pdf}
}

@article{ghorbani_fitting_2019,
	title = {Fitting of single-exhalation profiles using a pulmonary gas exchange model—application to carbon monoxide},
	volume = {13},
	issn = {1752-7163},
	url = {http://stacks.iop.org/1752-7163/13/i=2/a=026001?key=crossref.77c43ac78607c077f77fc2346df85db9},
	doi = {10.1088/1752-7163/aafc91},
	language = {en},
	number = {2},
	urldate = {2020-03-12},
	journal = {Journal of Breath Research},
	author = {Ghorbani, Ramin and Schmidt, Florian M},
	month = mar,
	year = {2019},
	pages = {026001},
	file = {Ghorbani et Schmidt - 2019 - Fitting of single-exhalation profiles using a pulm.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\7A236UH9\\Ghorbani et Schmidt - 2019 - Fitting of single-exhalation profiles using a pulm.pdf:application/pdf}
}

@article{lawal_exhaled_2017,
	title = {Exhaled breath analysis: a review of ‘breath-taking’ methods for off-line analysis},
	volume = {13},
	issn = {1573-3882, 1573-3890},
	shorttitle = {Exhaled breath analysis},
	url = {http://link.springer.com/10.1007/s11306-017-1241-8},
	doi = {10.1007/s11306-017-1241-8},
	abstract = {Methods  Literature search was carried out in databases MEDLINE, BIOSIS, EMBASE, INSPEC, COMPENDEX, PQSCITECH, and SCISEARCH using the STN platform which delivers peer-reviewed articles. Keywords searched for include breath, sampling, collection, pre-concentration, volatile. Forward and reverse search was then performed on initially included articles. The breath collection methodologies of all included articles was subsequently reviewed.
Results  Sampling methods differs between research groups, for example regarding the portion of breath being targeted. Definition of late expiratory breath varies between studies.
Conclusions  Breath analysis is an interdisciplinary field of study using clinical, analytical chemistry, data processing, and metabolomics expertise. A move towards standardisation in breath sampling is currently being promoted within the breath research community with a view to harmonising analysis and thereby increasing robustness and inter-laboratory comparisons.},
	language = {en},
	number = {10},
	urldate = {2020-03-12},
	journal = {Metabolomics},
	author = {Lawal, Oluwasola and Ahmed, Waqar M. and Nijsen, Tamara M. E. and Goodacre, Royston and Fowler, Stephen J.},
	month = oct,
	year = {2017},
	pages = {110},
	file = {Lawal et al. - 2017 - Exhaled breath analysis a review of ‘breath-takin.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\74XYU286\\Lawal et al. - 2017 - Exhaled breath analysis a review of ‘breath-takin.pdf:application/pdf}
}

@article{martin_modeling_2013,
	title = {Modeling of the oxygen transfer in the respiratory process},
	volume = {47},
	issn = {0764-583X, 1290-3841},
	url = {http://www.esaim-m2an.org/10.1051/m2an/2012052},
	doi = {10.1051/m2an/2012052},
	abstract = {In this article, we propose an integrated model for oxygen transfer into the blood, coupled with a lumped mechanical model for the ventilation process. Objectives. We aim at investigating oxygen transfer into the blood at rest or exercise. The ﬁrst task consists in describing nonlinear eﬀects of the oxygen transfer under normal conditions. We also include the possible diﬀusion limitation in oxygen transfer observed in extreme regimes involving parameters such as alveolar and venous blood oxygen partial pressures, capillary volume, diﬀusing capacity of the membrane, oxygen binding by hemoglobin and transit time of the red blood cells in the capillaries. The second task consists in discussing the oxygen concentration heterogeneity along the path length in the acinus. Method. A lumped mechanical model is considered: a double-balloon model is built upon physiological properties such as resistance of the branches connecting alveoli to the outside air, and elastic properties of the surrounding medium. Then, we focus on oxygen transfer: while the classical [F.J. Roughton and R.E. Forster, J. Appl. Physiol. 11 (1957) 290–302]. approach accounts for the reaction rate with hemoglobin by means of an extra resistance between alveolar air and blood, we propose an alternate description. Under normal conditions, the Hill’s saturation curve simply quantiﬁes the net oxygen transfer during the time that venous blood stays in the close neighborhood of alveoli (transit time). Under degraded and/or exercise conditions (impaired alveolar-capillary membrane, reduced transit time, high altitude) diﬀusion limitation of oxygen transfer is accounted for by means of the nonlinear equation representing the evolution of oxygen partial pressure in the plasma during the transit time. Finally, a one-dimensional model is proposed to investigate the eﬀects of longitudinal heterogeneity of oxygen concentration in the respiratory tract during the ventilation cycle, including previous considerations on oxygen transfer. Results. This integrated approach allows us to recover the right orders of magnitudes in terms of oxygen transfer, at rest or exercise, by using well-documented data, without any parameter tuning or curve ﬁtting procedure. The diﬀusing capacity of the alveolar-capillary membrane does not aﬀect the oxygen transfer rate in the normal regime but, as it decreases (e.g. because of emphysema) below a critical value, it becomes a signiﬁcant parameter. The one-dimensional model allows to investigate the screening phenomenon, i.e. the possibility that oxygen transfer might be signiﬁcantly aﬀected by the fact that the exchange area in the peripheral acinus poorly participates to oxygen transfer at rest, thereby providing a natural reserve of transfer capacity for exercise condition. We do not recover this eﬀect: in particular we show that, at rest, although the oxygen concentration is slightly smaller in terminal alveoli, transfer mainly occurs in the acinar periphery.},
	language = {en},
	number = {4},
	urldate = {2020-03-12},
	journal = {ESAIM: Mathematical Modelling and Numerical Analysis},
	author = {Martin, Sébastien and Maury, Bertrand},
	month = jul,
	year = {2013},
	pages = {935--960},
	file = {Martin et Maury - 2013 - Modeling of the oxygen transfer in the respiratory.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\WU6R88NK\\Martin et Maury - 2013 - Modeling of the oxygen transfer in the respiratory.pdf:application/pdf}
}

@article{cope_effects_2004,
	title = {Effects of ventilation on the collection of exhaled breath in humans},
	volume = {96},
	issn = {8750-7587, 1522-1601},
	url = {https://www.physiology.org/doi/10.1152/japplphysiol.01034.2003},
	doi = {10.1152/japplphysiol.01034.2003},
	abstract = {A computerized system has been developed to monitor tidal volume, respiration rate, mouth pressure, and carbon dioxide during breath collection. This system was used to investigate variability in the production of breath biomarkers over an 8-h period. Hyperventilation occurred when breath was collected from spontaneously breathing study subjects ( n = 8). Therefore, breath samples were collected from study subjects whose breathing were paced at a respiration rate of 10 breaths/min and whose tidal volumes were gauged according to body mass. In this “paced breathing” group ( n = 16), end-tidal concentrations of isoprene and ethane correlated with end-tidal carbon dioxide levels [Spearman's rank correlation test ( r
              s
              ) = 0.64, P = 0.008 and r
              s
              = 0.50, P = 0.05, respectively]. Ethane also correlated with heart rate ( r
              s
              = 0.52, P {\textless} 0.05). There was an inverse correlation between transcutaneous pulse oximetry and exhaled carbon monoxide ( r
              s
              = -0.64, P = 0.008). Significant differences were identified between men ( n = 8) and women ( n = 8) in the concentrations of carbon monoxide (4 parts per million in men vs. 3 parts per million in women; P = 0.01) and volatile sulfur-containing compounds (134 parts per billion in men vs. 95 parts per billion in women; P = 0.016). There was a peak in ethanol concentration directly after food consumption and a significant decrease in ethanol concentration 2 h later ( P = 0.01; n = 16). Sulfur-containing molecules increased linearly throughout the study period (β = 7.4, P {\textless} 0.003). Ventilation patterns strongly influence quantification of volatile analytes in exhaled breath and thus, accordingly, the breathing pattern should be controlled to ensure representative analyses.},
	language = {en},
	number = {4},
	urldate = {2020-03-13},
	journal = {Journal of Applied Physiology},
	author = {Cope, Keary A. and Watson, Michael T. and Foster, W. Michael and Sehnert, Shelley S. and Risby, Terence H.},
	month = apr,
	year = {2004},
	pages = {1371--1379},
	file = {Cope et al. - 2004 - Effects of ventilation on the collection of exhale.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\BQ6HGCSR\\Cope et al. - 2004 - Effects of ventilation on the collection of exhale.pdf:application/pdf}
}

@article{miekisch_diagnostic_2004-1,
	title = {Diagnostic potential of breath analysis—focus on volatile organic compounds},
	volume = {347},
	issn = {00098981},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0009898104002256},
	doi = {10.1016/j.cccn.2004.04.023},
	abstract = {Breath analysis has attracted a considerable amount of scientific and clinical interest during the last decade. In contrast to NO, which is predominantly generated in the bronchial system, volatile organic compounds (VOCs) are mainly blood borne and therefore enable monitoring of different processes in the body. Exhaled ethane and pentane concentrations were elevated in inflammatory diseases. Acetone was linked to dextrose metabolism and lipolysis. Exhaled isoprene concentrations showed correlations with cholesterol biosynthesis. Exhaled levels of sulphur-containing compounds were elevated in liver failure and allograft rejection. Looking at a set of volatile markers may enable recognition and diagnosis of complex diseases such as lung or breast cancer. Due to technical problems of sampling and analysis and a lack of normalization and standardization, huge variations exist between results of different studies. This is among the main reasons why breath analysis could not yet been introduced into clinical practice. This review addresses the basic principles of breath analysis and the diagnostic potential of different volatile breath markers. Analytical procedures, issues concerning biochemistry and exhalation mechanisms of volatile substances, and future developments will be discussed.},
	language = {en},
	number = {1-2},
	urldate = {2020-03-13},
	journal = {Clinica Chimica Acta},
	author = {Miekisch, Wolfram and Schubert, Jochen K and Noeldge-Schomburg, Gabriele F.E},
	month = sep,
	year = {2004},
	pages = {25--39},
	file = {Miekisch et al. - 2004 - Diagnostic potential of breath analysis—focus on v.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\YYM7NC77\\Miekisch et al. - 2004 - Diagnostic potential of breath analysis—focus on v.pdf:application/pdf}
}

@article{risby_current_2006,
	title = {Current status of clinical breath analysis},
	volume = {85},
	issn = {0946-2171, 1432-0649},
	url = {http://link.springer.com/10.1007/s00340-006-2280-4},
	doi = {10.1007/s00340-006-2280-4},
	abstract = {Clinical breath analysis remains in its infancy, despite the fact that its potential has been recognized for centuries and that blood, urine, and other bodily ﬂuids and tissues are routinely analyzed to diagnose disease or to monitor therapy. This review discusses the present status of clinical breath analysis and suggests reasons why breath analysis has not received similar widespread clinical use. Currently, a number of marker molecules have been identiﬁed in breath that could be used to identify disease, disease progression, or to monitor therapeutic intervention and this list is expected increase dramatically since the analysis of breath is ideally suited for population-based studies in the developed and underdeveloped world. Recent advances in analytical instrumentation have suggested that the use of exhaled breath in medicine should now be re-examined. In particular, the availability of real-time, portable monitors will represent a breakthrough for clinical diagnosis. Progress in clinical breath analysis will require collaboration amongst device makers, experts in breath analysis, and clinicians.},
	language = {en},
	number = {2-3},
	urldate = {2020-03-13},
	journal = {Applied Physics B},
	author = {Risby, T.H. and Solga, S.F.},
	month = nov,
	year = {2006},
	pages = {421--426},
	file = {Risby et Solga - 2006 - Current status of clinical breath analysis.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\7JJDIIH8\\Risby et Solga - 2006 - Current status of clinical breath analysis.pdf:application/pdf}
}

@article{karl_human_2001,
	title = {Human breath isoprene and its relation to blood cholesterol levels: new measurements and modeling},
	volume = {91},
	issn = {8750-7587, 1522-1601},
	shorttitle = {Human breath isoprene and its relation to blood cholesterol levels},
	url = {https://www.physiology.org/doi/10.1152/jappl.2001.91.2.762},
	doi = {10.1152/jappl.2001.91.2.762},
	abstract = {Numerous publications have described measurements of breath isoprene in humans, and there has been a hope that breath isoprene analyses could be a noninvasive diagnostic tool to assess blood cholesterol levels or cholesterol synthesis rate. However, significant analytic problems in breath isoprene analysis and variability in isoprene levels with age, exercise, diet, etc., have limited the usefulness of these measurements. Here, we have applied proton transfer reaction-mass spectrometry to this problem, allowing on-line detection of breath isoprene. We show that breath isoprene concentration increases within a few seconds after exercise is started as a result of a rapid increase in heart rate and then reaches a lower steady state when breath rate stabilizes. Additional experiments demonstrated that increases in heart rate associated with standing after reclining or sleeping are associated with increased breath isoprene concentrations. An isoprene gas-exchange model was developed and shows excellent fit to breath isoprene levels measured during exercise. In a preliminary experiment, we demonstrated that atorvastatin therapy leads to a decrease in serum cholesterol and low-density-lipoprotein levels and a parallel decrease in breath isoprene levels. This work suggests that there is constant endogenous production of isoprene during the day and night and reaffirms the possibility that breath isoprene can be a noninvasive marker of cholesterologenesis if care is taken to measure breath isoprene under standard conditions at constant heart rate.},
	language = {en},
	number = {2},
	urldate = {2020-03-13},
	journal = {Journal of Applied Physiology},
	author = {Karl, Thomas and Prazeller, Peter and Mayr, Dagmar and Jordan, Alfons and Rieder, Josef and Fall, Ray and Lindinger, Werner},
	month = aug,
	year = {2001},
	pages = {762--770},
	file = {Karl et al. - 2001 - Human breath isoprene and its relation to blood ch.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\5QNWXJ2F\\Karl et al. - 2001 - Human breath isoprene and its relation to blood ch.pdf:application/pdf}
}

@article{feinberg_cancer_2017,
	title = {Cancer metabolism: the volatile signature of glycolysis— \textit{in vitro} model in lung cancer cells},
	volume = {11},
	issn = {1752-7163},
	shorttitle = {Cancer metabolism},
	url = {http://stacks.iop.org/1752-7163/11/i=1/a=016008?key=crossref.61a59002babbe02b0bbedc1b2cb027c5},
	doi = {10.1088/1752-7163/aa51d6},
	abstract = {Discovering the volatile signature of cancer cells is an emerging approach in cancer research, as it may contribute to a fast and simple diagnosis of tumors in vivo and in vitro. One of the main contributors to such a volatile signature is hyperglycolysis, which characterizes the cancerous cell. The metabolic perturbation in cancer cells is known as the Warburg effect; glycolysis is preferred over oxidative phosphorylation (OXPHOS), even in the presence of oxygen. The precise mitochondrial alterations that underlie the increased dependence of cancer cells on aerobic glycolysis for energy generation have remained a mystery. We aimed to proﬁle the volatile signature of the glycolysis activity in lung cancer cells. For that an in vitro model, using lung cancer cell line cultures (A549, H2030, H358, H322), was developed. The volatile signature was measured by proton transfer reaction mass spectrometry under normal conditions and glycolysis inhibition. Glycolysis inhibition and mitochondrial activity were also assessed by mitochondrial respiration capacity measurements. Cells were divided into two groups upon their glycolytic proﬁle (PET positive and PET negative). Glycolysis blockade had a unique characteristic that was shared by all cells. Furthermore, each group had a characteristic volatile signature that enabled us to discriminate between those sub-groups of cells. In conclusion, lung cancer cells may have different subpopulations of cells upon low and high mitochondrial capacity. In both groups, glycolysis blockade induced a unique volatile signature.},
	language = {en},
	number = {1},
	urldate = {2020-03-14},
	journal = {Journal of Breath Research},
	author = {Feinberg, Tali and Herbig, Jens and Kohl, Ingrid and Las, Guy and Cancilla, John C and Torrecilla, Jose S and Ilouze, Maya and Haick, Hossam and Peled, Nir},
	month = jan,
	year = {2017},
	pages = {016008},
	file = {Feinberg et al. - 2017 - Cancer metabolism the volatile signature of glyco.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\PWVP4T9D\\Feinberg et al. - 2017 - Cancer metabolism the volatile signature of glyco.pdf:application/pdf}
}

@article{feinberg_cancerous_2016,
	title = {Cancerous glucose metabolism in lung cancer—evidence from exhaled breath analysis},
	volume = {10},
	issn = {1752-7163},
	url = {http://stacks.iop.org/1752-7163/10/i=2/a=026012?key=crossref.97777807ee893cbf5ee6bc696379891a},
	doi = {10.1088/1752-7155/10/2/026012},
	abstract = {Cancer cells prefer hyperglycolysis versus oxidative phosphorylation, even in the presence of oxygen. This phenomenon is used through the FDG-PET scans, and may affect the exhaled volatile signature. This study investigates the volatile signature in lung cancer (LC) before and after an oral glucose tolerance test (OGTT) to determine if tumor cells’ hyperglycolysis would affect the volatile signature. Blood glucose levels and exhaled breath samples were analyzed before the OGTT, and 90 min after, in both LC patients and controls. The volatile signature was measured by proton transfer reaction mass spectrometry (PTR-MS). Twenty-two LC patients (age 66.6  ±  12.7) with adenocarcinoma (n  =  14), squamous (n  =  6), small cell carcinoma (n  =  2), and twenty-one controls (age 54.4  ±  13.7; 10 non-smokers and 11 smokers) were included. All LC patients showed a hyperglycolytic state in their FDG-PET scans. Both baseline and post OGTT volatile signatures discriminate between the groups. The OGTT has a minimal effect in LC (a decrease in m/z 54 by 39\%, pv  =  0.0499); whereas in the control group, five masses (m/z 64, 87,88, 142 and 161) changed by  −13\%, −49\%, −40\% and  −29\% and 46\% respectively. To conclude, OGTT has a minimal effect on the VOC signature in LC patients, where a hyperglycolytic state already exists. In contrast, in the control group the OGTT has a profound effect in which induced hyperglycolysis significantly changed the VOC pattern. We hypothesized that a ceiling effect in cancerous patients is responsible for this discrepancy.},
	language = {en},
	number = {2},
	urldate = {2020-03-14},
	journal = {Journal of Breath Research},
	author = {Feinberg, Tali and Alkoby-Meshulam, Layah and Herbig, Jens and Cancilla, John C and Torrecilla, Jose S and Gai Mor, Naomi and Bar, Jair and Ilouze, Maya and Haick, Hossam and Peled, Nir},
	month = jun,
	year = {2016},
	pages = {026012},
	file = {Feinberg et al. - 2016 - Cancerous glucose metabolism in lung cancer—eviden.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\A7T46UN8\\Feinberg et al. - 2016 - Cancerous glucose metabolism in lung cancer—eviden.pdf:application/pdf}
}

@article{smith_mass_2014,
	title = {Mass spectrometry for real-time quantitative breath analysis},
	volume = {8},
	issn = {1752-7155, 1752-7163},
	url = {http://stacks.iop.org/1752-7163/8/i=2/a=027101?key=crossref.947798b7ff37f376a62a261671408ec5},
	doi = {10.1088/1752-7155/8/2/027101},
	abstract = {Breath analysis research is being successfully pursued using a variety of analytical methods, prominent amongst which are gas chromatography with mass spectrometry, GC-MS, ion mobility spectrometry, IMS, and the fast ﬂow and ﬂow-drift tube techniques called selected ion ﬂow tube mass spectrometry, SIFT-MS, and proton transfer reaction mass spectrometry, PTR-MS. In this paper the case is made for real-time breath analysis by obviating sample collection into bags or onto traps that can suffer from partial degradation of breath metabolites or the introduction of impurities. Real-time analysis of a broad range of volatile chemical compounds can be best achieved using SIFT-MS and PTR-MS, which are sufﬁciently sensitive and rapid to allow the simultaneous analyses of several trace gas metabolites in single breath exhalations. The basic principles and the ion chemistry that underpin these two analytical techniques are brieﬂy described and the differences between them, including their respective strengths and weaknesses, are revealed, especially with reference to the analysis of the complex matrix that is exhaled breath. A recent innovation is described that combines time-of-ﬂight mass spectrometry with the proton transfer ﬂow-drift tube reactor, PTR-TOFMS, which provides greater resolution in the analytical mass spectrometer and allows separation of protonated isobaric molecules. Examples are presented of some recent data that well illustrate the quality and real-time feature of SIFT-MS and PTR-MS for the analysis of exhaled breath for physiological/biochemical/pharmacokinetics studies and for the identiﬁcation and quantiﬁcation of biomarkers relating to speciﬁc disease states.},
	language = {en},
	number = {2},
	urldate = {2020-03-14},
	journal = {Journal of Breath Research},
	author = {Smith, David and Španěl, Patrik and Herbig, Jens and Beauchamp, Jonathan},
	month = mar,
	year = {2014},
	pages = {027101},
	file = {Smith et al. - 2014 - Mass spectrometry for real-time quantitative breat.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\ZWAMC2FZ\\Smith et al. - 2014 - Mass spectrometry for real-time quantitative breat.pdf:application/pdf}
}

@article{karl_human_2001-1,
	title = {Human breath isoprene and its relation to blood cholesterol levels: new measurements and modeling},
	volume = {91},
	issn = {8750-7587, 1522-1601},
	shorttitle = {Human breath isoprene and its relation to blood cholesterol levels},
	url = {https://www.physiology.org/doi/10.1152/jappl.2001.91.2.762},
	doi = {10.1152/jappl.2001.91.2.762},
	abstract = {Numerous publications have described measurements of breath isoprene in humans, and there has been a hope that breath isoprene analyses could be a noninvasive diagnostic tool to assess blood cholesterol levels or cholesterol synthesis rate. However, significant analytic problems in breath isoprene analysis and variability in isoprene levels with age, exercise, diet, etc., have limited the usefulness of these measurements. Here, we have applied proton transfer reaction-mass spectrometry to this problem, allowing on-line detection of breath isoprene. We show that breath isoprene concentration increases within a few seconds after exercise is started as a result of a rapid increase in heart rate and then reaches a lower steady state when breath rate stabilizes. Additional experiments demonstrated that increases in heart rate associated with standing after reclining or sleeping are associated with increased breath isoprene concentrations. An isoprene gas-exchange model was developed and shows excellent fit to breath isoprene levels measured during exercise. In a preliminary experiment, we demonstrated that atorvastatin therapy leads to a decrease in serum cholesterol and low-density-lipoprotein levels and a parallel decrease in breath isoprene levels. This work suggests that there is constant endogenous production of isoprene during the day and night and reaffirms the possibility that breath isoprene can be a noninvasive marker of cholesterologenesis if care is taken to measure breath isoprene under standard conditions at constant heart rate.},
	language = {en},
	number = {2},
	urldate = {2020-03-14},
	journal = {Journal of Applied Physiology},
	author = {Karl, Thomas and Prazeller, Peter and Mayr, Dagmar and Jordan, Alfons and Rieder, Josef and Fall, Ray and Lindinger, Werner},
	month = aug,
	year = {2001},
	pages = {762--770},
	file = {Karl et al. - 2001 - Human breath isoprene and its relation to blood ch.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\2FVJXNBE\\Karl et al. - 2001 - Human breath isoprene and its relation to blood ch.pdf:application/pdf}
}

@article{schubert_co_2001,
	title = {{CO} $_{\textrm{2}}$ -controlled sampling of alveolar gas in mechanically ventilated patients},
	volume = {90},
	issn = {8750-7587, 1522-1601},
	url = {https://www.physiology.org/doi/10.1152/jappl.2001.90.2.486},
	doi = {10.1152/jappl.2001.90.2.486},
	abstract = {A newly designed gas-sampling device using end-tidal CO
              2
              to separate dead space gas from alveolar gas was evaluated in 12 mechanically ventilated patients. For that purpose, CO
              2
              -controlled sampling was compared with mixed expiratory sampling. Alveolar sampling valves were easily controlled via CO
              2
              concentration. Concentrations of four volatile substances were determined in the expired and inspired gas. Isoflurane and isoprene, which did not occur in the inspired air, had ratios of end-tidal to mixed expired concentrations of 1.75 and 1.81, respectively. Acetone and pentane, found in both the inspired and expired air, showed ratios of 0.96 and 1.0, respectively. Precision of concentration measurements was between 2.4\% (isoprene) and 11.2\% (isoflurane); reproducibility (as coefficient of variation) was 5\%. Because the only possible source of isoflurane and isoprene in this setting was patients' blood, selective enrichment of alveolar gas was demonstrated. By using the new sampling technique, sensitivity of breath analysis was nearly doubled.},
	language = {en},
	number = {2},
	urldate = {2020-03-14},
	journal = {Journal of Applied Physiology},
	author = {Schubert, Jochen K. and Spittler, Karl-Heinz and Braun, Guenther and Geiger, Klaus and Guttmann, Josef},
	month = feb,
	year = {2001},
	pages = {486--492},
	file = {Schubert et al. - 2001 - CO sub2sub -controlled sampling of alveolar g.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\NRHARZWN\\Schubert et al. - 2001 - CO sub2sub -controlled sampling of alveolar g.pdf:application/pdf}
}

@article{koc_role_2011,
	title = {The role of mathematical modeling in {VOC} analysis using isoprene as a prototypic example},
	volume = {5},
	issn = {1752-7155, 1752-7163},
	url = {http://stacks.iop.org/1752-7163/5/i=3/a=037102?key=crossref.765442e9a1e0224e501c9eeaa33570b4},
	doi = {10.1088/1752-7155/5/3/037102},
	abstract = {Isoprene is one of the most abundant endogenous volatile organic compounds (VOCs) contained in human breath and is considered to be a potentially useful biomarker for diagnostic and monitoring purposes. However, neither the exact biochemical origin of isoprene nor its physiological role is understood in sufﬁcient depth, thus hindering the validation of breath isoprene tests in clinical routine. Exhaled isoprene concentrations are reported to change under different clinical and physiological conditions, especially in response to enhanced cardiovascular and respiratory activity. Investigating isoprene exhalation kinetics under dynamical exercise helps to gather the relevant experimental information for understanding the gas exchange phenomena associated with this important VOC. The ﬁrst model for isoprene in exhaled breath has been developed by our research group. In this paper, we aim at giving a concise overview of this model and describe its role in providing supportive evidence for a peripheral (extrahepatic) source of isoprene. In this sense, the results presented here may enable a new perspective on the biochemical processes governing isoprene formation in the human body.},
	language = {en},
	number = {3},
	urldate = {2020-03-14},
	journal = {Journal of Breath Research},
	author = {Koc, H and King, J and Teschl, G and Unterkofler, K and Teschl, S and Mochalski, P and Hinterhuber, H and Amann, A},
	month = sep,
	year = {2011},
	pages = {037102},
	file = {Koc et al. - 2011 - The role of mathematical modeling in VOC analysis .pdf:C\:\\Users\\CR258086\\Zotero\\storage\\ELNFHBR5\\Koc et al. - 2011 - The role of mathematical modeling in VOC analysis .pdf:application/pdf}
}

@article{king_physiological_2010,
	title = {Physiological modeling of isoprene dynamics in exhaled breath},
	volume = {267},
	issn = {00225193},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0022519310005023},
	doi = {10.1016/j.jtbi.2010.09.028},
	abstract = {Human breath contains a myriad of endogenous volatile organic compounds (VOCs) which are reﬂective of ongoing metabolic or physiological processes. While research into the diagnostic potential and general medical relevance of these trace gases is conducted on a considerable scale, little focus has been given so far to a sound analysis of the quantitative relationships between breath levels and the underlying systemic concentrations. This paper is devoted to a thorough modeling study of the end-tidal breath dynamics associated with isoprene, which serves as a paradigmatic example for the class of low-soluble, blood-borne VOCs.},
	language = {en},
	number = {4},
	urldate = {2020-03-14},
	journal = {Journal of Theoretical Biology},
	author = {King, Julian and Koc, Helin and Unterkofler, Karl and Mochalski, PaweŁ and Kupferthaler, Alexander and Teschl, Gerald and Teschl, Susanne and Hinterhuber, Hartmann and Amann, Anton},
	month = dec,
	year = {2010},
	pages = {626--637},
	file = {King et al. - 2010 - Physiological modeling of isoprene dynamics in exh.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\TRD95AK6\\King et al. - 2010 - Physiological modeling of isoprene dynamics in exh.pdf:application/pdf}
}

@article{beauchamp_real-time_2010,
	title = {Real-time breath gas analysis for pharmacokinetics: monitoring exhaled breath by on-line proton-transfer-reaction mass spectrometry after ingestion of eucalyptol-containing capsules},
	volume = {4},
	issn = {1752-7155, 1752-7163},
	shorttitle = {Real-time breath gas analysis for pharmacokinetics},
	url = {http://stacks.iop.org/1752-7163/4/i=2/a=026006?key=crossref.d3236173480b4b635f89bdb625877f0f},
	doi = {10.1088/1752-7155/4/2/026006},
	abstract = {Eucalyptol (1,8-cineole) is a common active agent in non-prescription pharmaceutical products that is employed to clear the airways during mucus blockages. Following ingestion of a eucalyptol-containing capsule, the capsule dissolves in the gut and transfers eucalyptol into the blood, which is subsequently expelled via the lungs, thus exposing this decongesting and inﬂammation-abating compound to the airways. The breath gas concentrations of eucalyptol in 11 healthy adult volunteers were monitored at regular intervals after capsule ingestion using on-line proton-transfer-reaction mass spectrometry (PTR-MS). Eucalyptol appeared in exhaled breath gas at varying times following ingestion, with its onset ranging from 1 h and 6 min to 4 h and 48 min (mean ± SD: 2.1 ± 0.5 h). Maximum concentrations also varied greatly, with peak eucalyptol levels between 106 and 1589 ppbv (mean ± SD: 489 ± 319 ppbv). These variations were not only inter-subject, but also intra-subject, i.e. repeated tests with the same participant yielded different onset times and a broad range of concentration maxima. A considerable contribution to these variations from infrequent sampling and analysis is discussed. This study characterized the temporal transfer of eucalyptol via the blood into the airways by examining exhaled breath and thereby demonstrated the suitability of on-line breath gas analyses, particularly PTR-MS, for certain pharmacokinetic investigations.},
	language = {en},
	number = {2},
	urldate = {2020-03-14},
	journal = {Journal of Breath Research},
	author = {Beauchamp, J and Kirsch, F and Buettner, A},
	month = jun,
	year = {2010},
	pages = {026006},
	file = {Beauchamp et al. - 2010 - Real-time breath gas analysis for pharmacokinetics.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\ZIKZWIN6\\Beauchamp et al. - 2010 - Real-time breath gas analysis for pharmacokinetics.pdf:application/pdf}
}

@article{winkler_real-time_2013,
	title = {Real-time metabolic monitoring with proton transfer reaction mass spectrometry},
	volume = {7},
	issn = {1752-7155, 1752-7163},
	url = {http://stacks.iop.org/1752-7163/7/i=3/a=036006?key=crossref.4875fc9cb40943af678e6c1f705e7a51},
	doi = {10.1088/1752-7155/7/3/036006},
	abstract = {We analysed the time evolution of several volatile organic compounds formed by the catabolism of ingested isotope-labelled ethanol using real-time breath gas analysis with proton-transfer-reaction mass spectrometry. Isotope labelling allowed distinguishing the emerging volatile metabolites from their naturally occurring, highly abundant counterparts in the human breath. Due to an extremely low detection limit of the employed technologies in the parts per trillion per volume range, it was possible to detect the emerging metabolic products in exhaled breath within ∼10 min after oral ingestion of isotope-labelled ethanol. We observed that ethanol was in part transformed into deuterated acetone and isoprene, reﬂecting the different fates of activated acetic acid (acetyl-coenzyme A), formed in ethanol metabolism. Using ethanol as a model clearly demonstrated the value of the here presented technique for the search for volatile markers for metabolic disorders in the exhaled breath and its potential usefulness in the diagnosis and monitoring of such diseases.},
	language = {en},
	number = {3},
	urldate = {2020-03-14},
	journal = {Journal of Breath Research},
	author = {Winkler, Klaus and Herbig, Jens and Kohl, Ingrid},
	month = aug,
	year = {2013},
	pages = {036006},
	file = {Winkler et al. - 2013 - Real-time metabolic monitoring with proton transfe.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\Q4969EPJ\\Winkler et al. - 2013 - Real-time metabolic monitoring with proton transfe.pdf:application/pdf}
}

@article{kohl_first_2013,
	title = {First observation of a potential non-invasive breath gas biomarker for kidney function},
	volume = {7},
	issn = {1752-7155, 1752-7163},
	url = {http://stacks.iop.org/1752-7163/7/i=1/a=017110?key=crossref.c5d74a3907d49d697065f50c60838a0a},
	doi = {10.1088/1752-7155/7/1/017110},
	language = {en},
	number = {1},
	urldate = {2020-03-14},
	journal = {Journal of Breath Research},
	author = {Kohl, Ingrid and Beauchamp, Jonathan and Cakar-Beck, Ferguel and Herbig, Jens and Dunkl, J and Tietje, Olaf and Tiefenthaler, Martin and Boesmueller, Claudia and Wisthaler, Armin and Breitenlechner, Martin and Langebner, Stephan and Zabernigg, August and Reinstaller, Florian and Winkler, Klaus and Gutmann, Rene and Hansel, Armin},
	month = feb,
	year = {2013},
	pages = {017110},
	file = {Kohl et al. - 2013 - First observation of a potential non-invasive brea.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\UVL2XER7\\Kohl et al. - 2013 - First observation of a potential non-invasive brea.pdf:application/pdf}
}

@article{miekisch_data_2012,
	title = {Data interpretation in breath biomarker research: pitfalls and directions},
	volume = {6},
	issn = {1752-7155, 1752-7163},
	shorttitle = {Data interpretation in breath biomarker research},
	url = {http://stacks.iop.org/1752-7163/6/i=3/a=036007?key=crossref.05eaf83b4b4b20424c143d1a0c6701b3},
	doi = {10.1088/1752-7155/6/3/036007},
	abstract = {Most—if not all—potential diagnostic applications in breath research involve different marker concentrations rather than unique breath markers which only occur in the diseased state. Hence, data interpretation is a crucial step in breath analysis. To avoid artiﬁcial signiﬁcance in breath testing every effort should be made to implement method validation, data cross-testing and statistical validation along this process. The most common data analysis related problems can be classiﬁed into three groups: confounding variables (CVs), which have a real correlation with both the diseased state and a breath marker but lead to the erroneous conclusion that disease and breath are in a causal relationship; voodoo correlations (VCs), which can be understood as statistically true correlations that arise coincidentally in the vast number of measured variables; and statistical misconceptions in the study design (SMSD). CV: Typical confounding variables are environmental and medical history, host factors such as gender, age, weight, etc and parameters that could affect the quality of breath data such as subject breathing mode, effects of breath sampling and effects of the analytical technique itself. VC: The number of measured variables quickly overwhelms the number of samples that can feasibly be taken. As a consequence, the chances of ﬁnding coincidental ‘voodoo’ correlations grow proportionally. VCs can typically be expected in the following scenarios: insufﬁcient number of patients, (too) many measurement variables, the use of advanced statistical data mining methods, and non-independent data for validation.},
	language = {en},
	number = {3},
	urldate = {2020-03-14},
	journal = {Journal of Breath Research},
	author = {Miekisch, Wolfram and Herbig, Jens and Schubert, Jochen K},
	month = sep,
	year = {2012},
	pages = {036007},
	file = {Miekisch et al. - 2012 - Data interpretation in breath biomarker research .pdf:C\:\\Users\\CR258086\\Zotero\\storage\\GTIMFB7M\\Miekisch et al. - 2012 - Data interpretation in breath biomarker research .pdf:application/pdf}
}

@article{herbig_towards_2014,
	title = {Towards standardization in the analysis of breath gas volatiles},
	volume = {8},
	issn = {1752-7155, 1752-7163},
	url = {http://stacks.iop.org/1752-7163/8/i=3/a=037101?key=crossref.4e3bdba7f2701356e225d9050ae0ae5e},
	doi = {10.1088/1752-7155/8/3/037101},
	abstract = {Despite growing interest and considerable progress in breath research over the last decade, standardized practices for the sampling and analysis of breath gas volatiles remain elusive. The primary reasons for this are (a) the rich chemical diversity of exhaled breath that covers an extensive range of volatile organic compounds at highly varied concentrations, (b) the vast disparity in the analytical tools employed, (c) diverse study goals and (d) the presence of (unidentiﬁed) confounders. These aspects place stringent but divergent demands on sampling and analysis: each analytical tool, target compound and concentration range requires its own speciﬁc protocol and in many cases the latter two are not even known a priori. The ongoing rapid developments and constant discoveries in the ﬁeld of breath research and the lack of established best practices in breath gas sampling and analysis currently preclude an acceptable overall standardization of these methods. This paper addresses these manifold issues and suggests a framework that separately considers individual stages of sampling and analysis with a view to establishing standardization in the analysis of breath gas volatiles to suit different target compounds and analytical technologies.},
	language = {en},
	number = {3},
	urldate = {2020-03-14},
	journal = {Journal of Breath Research},
	author = {Herbig, Jens and Beauchamp, Jonathan},
	month = sep,
	year = {2014},
	pages = {037101},
	file = {Herbig et Beauchamp - 2014 - Towards standardization in the analysis of breath .pdf:C\:\\Users\\CR258086\\Zotero\\storage\\I9BXJ3JB\\Herbig et Beauchamp - 2014 - Towards standardization in the analysis of breath .pdf:application/pdf}
}

@article{salvo_dual_2015,
	title = {A dual mode breath sampler for the collection of the end-tidal and dead space fractions},
	volume = {37},
	issn = {13504533},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1350453315000879},
	doi = {10.1016/j.medengphy.2015.03.013},
	abstract = {This work presents a breath sampler prototype automatically collecting end-tidal (single and multiple breaths) or dead space air fractions (multiple breaths). This result is achieved by real time measurements of the CO2 partial pressure and airﬂow during the expiratory and inspiratory phases. Suitable algorithms, used to control a solenoid valve, guarantee that a Nalophan R bag is ﬁlled with the selected breath fraction even if the subject under test hyperventilates. The breath sampler has low pressure drop ({\textless}0.5 kPa) and uses inert or disposable components to avoid bacteriological risk for the patients and contamination of the breath samples. A fully customisable software interface allows a real time control of the hardware and software status. The performances of the breath sampler were evaluated by comparing (a) the CO2 partial pressure calculated during the sampling with the CO2 pressure measured off-line within the Nalophan R bag; (b) the concentrations of four selected volatile organic compounds in dead space, end-tidal and mixed breath fractions.},
	language = {en},
	number = {6},
	urldate = {2020-03-17},
	journal = {Medical Engineering \& Physics},
	author = {Salvo, P. and Ferrari, C. and Persia, R. and Ghimenti, S. and Lomonaco, T. and Bellagambi, F. and Di Francesco, F.},
	month = jun,
	year = {2015},
	pages = {539--544},
	annote = {CO2 visual limit
CO2 sensor captogram},
	file = {Salvo et al. - 2015 - A dual mode breath sampler for the collection of t.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\M8KQZMRM\\Salvo et al. - 2015 - A dual mode breath sampler for the collection of t.pdf:application/pdf}
}

@article{weber_volatile_2020,
	title = {Volatile organic compound breath signatures of children with cystic fibrosis by real-time {SESI}-{HRMS}},
	volume = {6},
	issn = {2312-0541},
	url = {http://openres.ersjournals.com/lookup/doi/10.1183/23120541.00171-2019},
	doi = {10.1183/23120541.00171-2019},
	abstract = {Early pulmonary infection and inflammation result in irreversible lung damage and are major contributors to cystic fibrosis (CF)-related morbidity. An easy to apply and noninvasive assessment for the timely detection of disease-associated complications would be of high value. We aimed to detect volatile organic compound (VOC) breath signatures of children with CF by real-time secondary electrospray ionisation high-resolution mass spectrometry (SESI-HRMS).},
	language = {en},
	number = {1},
	urldate = {2020-03-18},
	journal = {ERJ Open Research},
	author = {Weber, Ronja and Haas, Naemi and Baghdasaryan, Astghik and Bruderer, Tobias and Inci, Demet and Micic, Srdjan and Perkins, Nathan and Spinas, Renate and Zenobi, Renato and Moeller, Alexander},
	month = jan,
	year = {2020},
	pages = {00171--2019},
	file = {Weber et al. - 2020 - Volatile organic compound breath signatures of chi.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\TR7DYRRH\\Weber et al. - 2020 - Volatile organic compound breath signatures of chi.pdf:application/pdf}
}

@article{anderson_breath_2007,
	title = {Breath tests and airway gas exchange},
	volume = {20},
	issn = {10945539},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1094553905001641},
	doi = {10.1016/j.pupt.2005.12.002},
	abstract = {Measuring soluble gas in the exhaled breath is a non-invasive technique used to estimate levels of respiratory, solvent, and metabolic gases. The interpretation of these measurements is based on the assumption that the measured gases exchange in the alveoli. While the respiratory gases have a low blood-solubility and exchange in the alveoli, high blood-soluble gases exchange in the airways. The effect of airway gas exchange on the interpretation of these exhaled breath measurements can be signiﬁcant. We describe airway gas exchange in relation to exhaled measurements of soluble gases that exchange in the alveoli. The mechanisms of airway gas exchange are reviewed and criteria for determining if a gas exchanges in the airways are provided. The effects of diffusion, perfusion, temperature and breathing maneuver on airway gas exchange and on measurement of exhaled soluble gas are discussed. A method for estimating the impact of airway gas exchange on exhaled breath measurements is presented. We recommend that investigators should carefully control the inspired air conditions and type of exhalation maneuver used in a breath test. Additionally, care should be taken when interpreting breath tests from subjects with pulmonary disease.},
	language = {en},
	number = {2},
	urldate = {2020-03-18},
	journal = {Pulmonary Pharmacology \& Therapeutics},
	author = {Anderson, Joseph C. and Hlastala, Michael P.},
	month = apr,
	year = {2007},
	pages = {112--117},
	file = {Anderson et Hlastala - 2007 - Breath tests and airway gas exchange.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\SJHZ9VFN\\Anderson et Hlastala - 2007 - Breath tests and airway gas exchange.pdf:application/pdf}
}

@article{anderson_modeling_2003,
	title = {Modeling {Soluble} {Gas} {Exchange} in the {Airways} and {Alveoli}},
	volume = {31},
	issn = {0090-6964},
	url = {http://link.springer.com/10.1114/1.1630600},
	doi = {10.1114/1.1630600},
	abstract = {A mathematical model of heat, water and soluble gas exchange in the airways and alveoli was used to predict the location of soluble gas exchange in the lung. A previously published model of heat, water and soluble gas exchange in the airways was improved by incorporating anatomical data on the airway wall to better describe the bronchial circulation and expanding the model to include a time varying description of soluble gas concentration in the alveoli. Next, the model was validated using two experimental data sets from the literature: ͑1͒ ethanol expirograms and ͑2͒ the uptake of seven soluble gases. Then, the model simulated the excretion of ten soluble gases whose blood:air partition coefﬁcient (␭b:a), a measure of blood solubility, ranged over 5 orders of magnitude. We found that gases with ␭b:aϽ10 exchange almost solely in the alveoli and gases with ␭b:aϾ100 exchange almost exclusively in the airways. Gases with ␭b:a between 10 and 100 have signiﬁcant interaction with the airways and alveoli. These results suggest that the airways play a larger role in pulmonary gas exchange than previously assumed and may require a reevaluation of pulmonary tests that involve exhaled samples of gases with ␭b:aϾ10. © 2003 Biomedical Engineering Society.},
	language = {en},
	number = {11},
	urldate = {2020-03-19},
	journal = {Annals of Biomedical Engineering},
	author = {Anderson, Joseph C. and Babb, Albert L. and Hlastala, Michael P.},
	month = dec,
	year = {2003},
	pages = {1402--1422},
	file = {Anderson et al. - 2003 - Modeling Soluble Gas Exchange in the Airways and A.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\TRMT85T5\\Anderson et al. - 2003 - Modeling Soluble Gas Exchange in the Airways and A.pdf:application/pdf}
}

@article{brock_monitoring_2017,
	title = {Monitoring of breath {VOCs} and electrical impedance tomography under pulmonary recruitment in mechanically ventilated patients},
	volume = {11},
	issn = {1752-7163},
	url = {https://iopscience.iop.org/article/10.1088/1752-7163/aa53b2},
	doi = {10.1088/1752-7163/aa53b2},
	abstract = {Analysis of exhaled VOCs can provide information on physiology, metabolic processes, oxidative stress and lung diseases. In critically ill patients, VOC analysis may be used to gain complimentary information beyond global clinical parameters. This seems especially attractive in mechanically ventilated patients frequently suffering from impairment of gas exchange. This study was intended to assess (a) the effects of recruitment maneuvers onto VOC proﬁles, (b) the correlations between electrical impedance tomography (EIT) data and VOC proﬁles and (c) the effects of recruitment onto distribution of ventilation. Eleven mechanically ventilated patients were investigated during lung recruitment after cardiac surgery. Continuous breath gas analysis by means of PTR-ToF-MS, EIT and blood gas analyses were performed simultaneously. More than 300 mass traces could be detected and monitored continuously by means of PTR-ToF-MS in every patient. Exhaled VOC concentrations varied with recruitment induced changes in minute ventilation and cardiac output. Ammonia exhalation depended on blood pH. The improvement in dorsal lung ventilation during recruitment ranged from 9\% to 110\%. Correlations between exhaled concentrations of acetone, isoprene, benzene sevoﬂurane and improvement in regional ventilation during recruitment were observed. Extent and quality of these correlations depended on physico-chemical properties of the VOCs. Combination of continuous real-time breath analysis and EIT revealed correlations between exhaled VOC concentrations and distribution of ventilation. This setup enabled immediate recognition of physiological and therapeutic effects in ICU patients. In a perspective, VOC analysis could be used for non-invasive control and optimization of ventilation strategies.},
	language = {en},
	number = {1},
	urldate = {2020-03-19},
	journal = {Journal of Breath Research},
	author = {Brock, Beate and Kamysek, Svend and Silz, Josephine and Trefz, Phillip and Schubert, Jochen K and Miekisch, Wolfram},
	month = jan,
	year = {2017},
	pages = {016005},
	file = {Brock et al. - 2017 - Monitoring of breath VOCs and electrical impedance.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\YQWHCGA9\\Brock et al. - 2017 - Monitoring of breath VOCs and electrical impedance.pdf:application/pdf}
}

@article{graus_high_2010-1,
	title = {High resolution {PTR}-{TOF}: {Quantification} and formula confirmation of {VOC} in real time},
	volume = {21},
	issn = {1044-0305, 1879-1123},
	shorttitle = {High resolution {PTR}-{TOF}},
	url = {https://pubs.acs.org/doi/10.1021/jasms.8b03774},
	doi = {10.1016/j.jasms.2010.02.006},
	language = {en},
	number = {6},
	urldate = {2020-03-19},
	journal = {Journal of the American Society for Mass Spectrometry},
	author = {Graus, Martin and Müller, Markus and Hansel, Armin},
	month = jun,
	year = {2010},
	pages = {1037--1044},
	file = {Graus et al. - 2010 - High resolution PTR-TOF Quantification and formul.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\GULNL625\\Graus et al. - 2010 - High resolution PTR-TOF Quantification and formul.pdf:application/pdf}
}

@article{blake_demonstration_2004-2,
	title = {Demonstration of {Proton}-{Transfer} {Reaction} {Time}-of-{Flight} {Mass} {Spectrometry} for {Real}-{Time} {Analysis} of {Trace} {Volatile} {Organic} {Compounds}},
	volume = {76},
	issn = {0003-2700, 1520-6882},
	url = {https://pubs.acs.org/doi/10.1021/ac0498260},
	doi = {10.1021/ac0498260},
	language = {en},
	number = {13},
	urldate = {2020-03-19},
	journal = {Analytical Chemistry},
	author = {Blake, Robert S. and Whyte, Christopher and Hughes, Ceri O. and Ellis, Andrew M. and Monks, Paul S.},
	month = jul,
	year = {2004},
	pages = {3841--3845},
	file = {Blake et al. - 2004 - Demonstration of Proton-Transfer Reaction Time-of-.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\S67ZM3UC\\Blake et al. - 2004 - Demonstration of Proton-Transfer Reaction Time-of-.pdf:application/pdf}
}

@article{trefz_effects_2019,
	title = {Effects of elevated oxygen levels on {VOC} analysis by means of {PTR}-{ToF}-{MS}},
	volume = {13},
	issn = {1752-7163},
	url = {https://iopscience.iop.org/article/10.1088/1752-7163/ab28ec},
	doi = {10.1088/1752-7163/ab28ec},
	abstract = {Proton-transfer-reaction-time-of-ﬂight-mass-spectrometry (PTR-ToF-MS) is a powerful tool for real-time monitoring of volatile organic compound (VOC) proﬁles in human breath. However, varying oxygen concentrations in the sample matrix may inﬂuence results from VOC analysis by PTRToF-MS. Elevated oxygen concentrations are likely to occur in clinical settings, but also when respiratory masks or breathing apparatus are used (e.g. in scuba diving, aviation, ﬁreﬁghting). Oxygen concentration may vary between subjects or within the course of a measurement or study and thus bias results. We systematically assessed the effect of high O2 concentrations (up to 90\%) in the sample matrix on the results of PTR-MS analysis for a pattern of VOCs including aromatics, aldehydes and ketones in dry and humid samples. In vivo experiments in healthy volunteers and mechanically ventilated animals were done to test the effect under real-life conditions. H3O+ count signiﬁcantly decreased by more than 40\% when the amount of oxygen in the sample matrix was increased. Almost all investigated VOCs were signiﬁcantly effected by varying oxygen concentrations and differences in signal intensities of more than 50\% could be observed. The effect was generally more pronounced in dry samples but still signiﬁcant under humid conditions. A linear dependency of sensitivity on the oxygen concentration in the sample matrix was observed for a number of VOCs (e.g. aldehydes) possibly enabling a factor based correction. VOC intensities were also inﬂuenced under in vivo conditions, e.g. ethanol decreased up to 71\%. When PTR-MS analysis is carried out under oxygen supply, these issues need to be carefully considered.},
	language = {en},
	number = {4},
	urldate = {2020-03-19},
	journal = {Journal of Breath Research},
	author = {Trefz, Phillip and Pugliese, Giovanni and Brock, Beate and Schubert, Jochen K and Miekisch, Wolfram},
	month = jul,
	year = {2019},
	pages = {046004},
	file = {Trefz et al. - 2019 - Effects of elevated oxygen levels on VOC analysis .pdf:C\:\\Users\\CR258086\\Zotero\\storage\\B3D68SS4\\Trefz et al. - 2019 - Effects of elevated oxygen levels on VOC analysis .pdf:application/pdf}
}

@article{korovesi_exhaled_2011,
	title = {Exhaled {Breath} {Condensate} in {Mechanically} {Ventilated} {Brain}-injured {Patients} with {No} {Lung} {Injury} or {Sepsis}:},
	volume = {114},
	issn = {0003-3022},
	shorttitle = {Exhaled {Breath} {Condensate} in {Mechanically} {Ventilated} {Brain}-injured {Patients} with {No} {Lung} {Injury} or {Sepsis}},
	url = {http://content.wkhealth.com/linkback/openurl?sid=WKPTLP:landingpage&an=00000542-201105000-00022},
	doi = {10.1097/ALN.0b013e31820d84db},
	abstract = {Background: The inflammatory influence of prolonged mechanical ventilation in uninjured lungs remains a matter of controversy and largely unexplored in humans. The authors investigated pulmonary inflammation by using exhaled breath condensate (EBC) in mechanically ventilated, brain-injured patients in the absence of acute lung injury or sepsis and explored the potential influence of positive end-expiratory pressure (PEEP).},
	language = {en},
	number = {5},
	urldate = {2020-03-19},
	journal = {Anesthesiology},
	author = {Korovesi, Ioanna and Papadomichelakis, Evangelos and Orfanos, Stylianos E. and Giamarellos-Bourboulis, Evangellos J. and Livaditi, Olga and Pelekanou, Aimilia and Sotiropoulou, Christina and Koutsoukou, Antonia and Dimopoulou, Ioanna and Ekonomidou, Foteini and Psevdi, Ekaterini and Armaganidis, Apostolos and Roussos, Charis and Marczin, Nandor and Kotanidou, Anastasia},
	month = may,
	year = {2011},
	pages = {1118--1129},
	file = {Korovesi et al. - 2011 - Exhaled Breath Condensate in Mechanically Ventilat.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\YI7VGI5E\\Korovesi et al. - 2011 - Exhaled Breath Condensate in Mechanically Ventilat.pdf:application/pdf}
}

@article{wan_particle_2014,
	title = {Particle {Size} {Concentration} {Distribution} and {Influences} on {Exhaled} {Breath} {Particles} in {Mechanically} {Ventilated} {Patients}},
	volume = {9},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0087088},
	doi = {10.1371/journal.pone.0087088},
	abstract = {Humans produce exhaled breath particles (EBPs) during various breath activities, such as normal breathing, coughing, talking, and sneezing. Airborne transmission risk exists when EBPs have attached pathogens. Until recently, few investigations had evaluated the size and concentration distributions of EBPs from mechanically ventilated patients with different ventilation mode settings. This study thus broke new ground by not only evaluating the size concentration distributions of EBPs in mechanically ventilated patients, but also investigating the relationship between EBP level and positive expiratory end airway pressure (PEEP), tidal volume, and pneumonia. This investigation recruited mechanically ventilated patients, with and without pneumonia, aged 20 years old and above, from the respiratory intensive care unit of a medical center. Concentration distributions of EBPs from mechanically ventilated patients were analyzed with an optical particle analyzer. This study finds that EBP concentrations from mechanically ventilated patients during normal breathing were in the range 0.47–2,554.04 particles/breath (0.001–4.644 particles/mL). EBP concentrations did not differ significantly between the volume control and pressure control modes of the ventilation settings in the mechanically ventilated patients. The patient EBPs were sized below 5 mm, and 80\% of them ranged from 0.3 to 1.0 mm. The EBPs concentrations in patients with high PEEP (. 5 cmH2O) clearly exceeded those in patients with low PEEP (\# 5 cmH2O). Additionally, a significant negative association existed between pneumonia duration and EBPs concentration. However, tidal volume was not related to EBPs concentration.},
	language = {en},
	number = {1},
	urldate = {2020-03-19},
	journal = {PLoS ONE},
	author = {Wan, Gwo-Hwa and Wu, Chieh-Liang and Chen, Yi-Fang and Huang, Sheng-Hsiu and Wang, Yu-Ling and Chen, Chun-Wan},
	editor = {Tang, Julian W.},
	month = jan,
	year = {2014},
	pages = {e87088},
	file = {Wan et al. - 2014 - Particle Size Concentration Distribution and Influ.PDF:C\:\\Users\\CR258086\\Zotero\\storage\\2UN22LGM\\Wan et al. - 2014 - Particle Size Concentration Distribution and Influ.PDF:application/pdf}
}

@article{bos_simple_2014,
	title = {A simple breath sampling method in intubated and mechanically ventilated critically ill patients},
	volume = {191},
	issn = {15699048},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1569904813003674},
	doi = {10.1016/j.resp.2013.11.001},
	abstract = {Volatile organic compounds (VOCs) in breath may serve as biomarkers of pulmonary infection or inﬂammation. We developed and validated a new breath sampling method for VOC analysis in ventilated patients.},
	language = {en},
	urldate = {2020-03-19},
	journal = {Respiratory Physiology \& Neurobiology},
	author = {Bos, Lieuwe D.J. and Wang, Yuanyue and Weda, Hans and Nijsen, Tamara M.E. and Janssen, Anton P.G.E. and Knobel, Hugo H. and Vink, Teunis J. and Schultz, Marcus J. and Sterk, Peter J.},
	month = jan,
	year = {2014},
	pages = {67--74},
	file = {Bos et al. - 2014 - A simple breath sampling method in intubated and m.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\BZPFZTVW\\Bos et al. - 2014 - A simple breath sampling method in intubated and m.pdf:application/pdf}
}

@article{carter_exhaled_2012,
	title = {Exhaled breath condensate collection in the mechanically ventilated patient},
	volume = {106},
	issn = {09546111},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0954611112000716},
	doi = {10.1016/j.rmed.2012.02.003},
	abstract = {Collection of exhaled breath condensate (EBC) is a non-invasive means of sampling the airwaylining ﬂuid of the lungs. EBC contains numerous measurable mediators, whose analysis could change the management of patients with certain pulmonary diseases.},
	language = {en},
	number = {5},
	urldate = {2020-03-19},
	journal = {Respiratory Medicine},
	author = {Carter, Stewart R. and Davis, Christopher S. and Kovacs, Elizabeth J.},
	month = may,
	year = {2012},
	pages = {601--613},
	file = {Carter et al. - 2012 - Exhaled breath condensate collection in the mechan.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\R6ASU935\\Carter et al. - 2012 - Exhaled breath condensate collection in the mechan.pdf:application/pdf}
}

@article{roca_mechanical_2010,
	title = {Mechanical ventilation induces changes in exhaled breath condensate of patients without lung injury},
	volume = {104},
	issn = {09546111},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0954611110000387},
	doi = {10.1016/j.rmed.2010.01.013},
	abstract = {Introduction: Measurement of biomarkers in exhaled breath condensate (EBC) may be useful for monitoring lung inﬂammation and injury in mechanically ventilated patients. The aim of this study was to analyze changes in biomarkers of inﬂammation in EBC associated with prolonged mechanical ventilation.},
	language = {en},
	number = {6},
	urldate = {2020-03-19},
	journal = {Respiratory Medicine},
	author = {Roca, Oriol and Gómez-Ollés, Susana and Cruz, Maria-Jesús and Muñoz, Xavier and Griffiths, Mark J.D. and Masclans, Joan R.},
	month = jun,
	year = {2010},
	pages = {822--828},
	file = {Roca et al. - 2010 - Mechanical ventilation induces changes in exhaled .pdf:C\:\\Users\\CR258086\\Zotero\\storage\\QXYQKBSY\\Roca et al. - 2010 - Mechanical ventilation induces changes in exhaled .pdf:application/pdf}
}

@article{breit_modeling_2015,
	title = {Modeling and {Classification} of {Kinetic} {Patterns} of {Dynamic} {Metabolic} {Biomarkers} in {Physical} {Activity}},
	volume = {11},
	issn = {1553-7358},
	url = {http://dx.plos.org/10.1371/journal.pcbi.1004454},
	doi = {10.1371/journal.pcbi.1004454},
	language = {en},
	number = {8},
	urldate = {2020-03-23},
	journal = {PLOS Computational Biology},
	author = {Breit, Marc and Netzer, Michael and Weinberger, Klaus M. and Baumgartner, Christian},
	editor = {Ouzounis, Christos A.},
	month = aug,
	year = {2015},
	pages = {e1004454},
	file = {Breit et al. - 2015 - Modeling and Classification of Kinetic Patterns of.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\CI4564YD\\Breit et al. - 2015 - Modeling and Classification of Kinetic Patterns of.pdf:application/pdf}
}

@article{berk_statistical_2011,
	title = {A statistical framework for biomarker discovery in metabolomic time course data},
	volume = {27},
	issn = {1367-4803, 1460-2059},
	url = {https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btr289},
	doi = {10.1093/bioinformatics/btr289},
	abstract = {Motivation: Metabolomics is the study of the complement of small molecule metabolites in cells, bioﬂuids and tissues. Many metabolomic experiments are designed to compare changes observed over time under two experimental conditions or groups (e.g. a control and drug-treated group) with the goal of identifying discriminatory metabolites or biomarkers that characterize each condition. A common study design consists of repeated measurements taken on each experimental unit thus producing time courses of all metabolites. We describe a statistical framework for estimating time-varying metabolic proﬁles and their within-group variability and for detecting between-group differences. Speciﬁcally, we propose (i) a smoothing splines mixed effects (SME) model that treats each longitudinal measurement as a smooth function of time and (ii) an associated functional test statistic. Statistical signiﬁcance is assessed by a non-parametric bootstrap procedure.},
	language = {en},
	number = {14},
	urldate = {2020-03-23},
	journal = {Bioinformatics},
	author = {Berk, Maurice and Ebbels, Timothy and Montana, Giovanni},
	month = jul,
	year = {2011},
	pages = {1979--1985},
	file = {Berk et al. - 2011 - A statistical framework for biomarker discovery in.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\H42UF6X2\\Berk et al. - 2011 - A statistical framework for biomarker discovery in.pdf:application/pdf}
}

@article{jendoubi_integrative_2020,
	title = {Integrative analysis of time course metabolic data and biomarker discovery},
	volume = {21},
	issn = {1471-2105},
	url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3333-0},
	doi = {10.1186/s12859-019-3333-0},
	abstract = {Background: Metabolomics time-course experiments provide the opportunity to understand the changes to an organism by observing the evolution of metabolic profiles in response to internal or external stimuli. Along with other omic longitudinal profiling technologies, these techniques have great potential to uncover complex relations between variations across diverse omic variables and provide unique insights into the underlying biology of the system. However, many statistical methods currently used to analyse short time-series omic data are i) prone to overfitting, ii) do not fully take into account the experimental design or iii) do not make full use of the multivariate information intrinsic to the data or iv) are unable to uncover multiple associations between different omic data. The model we propose is an attempt to i) overcome overfitting by using a weakly informative Bayesian model, ii) capture experimental design conditions through a mixed-effects model, iii) model interdependencies between variables by augmenting the mixed-effects model with a conditional auto-regressive (CAR) component and iv) identify potential associations between heterogeneous omic variables by using a horseshoe prior.
Results: We assess the performance of our model on synthetic and real datasets and show that it can outperform comparable models for metabolomic longitudinal data analysis. In addition, our proposed method provides the analyst with new insights on the data as it is able to identify metabolic biomarkers related to treatment, infer perturbed pathways as a result of treatment and find significant associations with additional omic variables. We also show through simulation that our model is fairly robust against inaccuracies in metabolite assignments. On real data, we demonstrate that the number of profiled metabolites slightly affects the predictive ability of the model.
Conclusions: Our single model approach to longitudinal analysis of metabolomics data provides an approach simultaneously for integrative analysis and biomarker discovery. In addition, it lends better interpretation by allowing analysis at the pathway level. An accompanying R package for the model has been developed using the probabilistic programming language Stan. The package offers user-friendly functions for simulating data, fitting the model, assessing model fit and postprocessing the results. The main aim of the R package is to offer freely accessible resources for integrative longitudinal analysis for metabolomics scientists and various visualization functions easy-to-use for applied researchers to interpret results.},
	language = {en},
	number = {1},
	urldate = {2020-03-23},
	journal = {BMC Bioinformatics},
	author = {Jendoubi, Takoua and Ebbels, Timothy M. D.},
	month = dec,
	year = {2020},
	pages = {11},
	file = {Jendoubi et Ebbels - 2020 - Integrative analysis of time course metabolic data.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\ZZQC93VU\\Jendoubi et Ebbels - 2020 - Integrative analysis of time course metabolic data.pdf:application/pdf}
}

@article{straube_linear_2015,
	title = {A {Linear} {Mixed} {Model} {Spline} {Framework} for {Analysing} {Time} {Course} ‘{Omics}’ {Data}},
	volume = {10},
	issn = {1932-6203},
	url = {http://dx.plos.org/10.1371/journal.pone.0134540},
	doi = {10.1371/journal.pone.0134540},
	abstract = {Time course ‘omics’ experiments are becoming increasingly important to study systemwide dynamic regulation. Despite their high information content, analysis remains challenging. ‘Omics’ technologies capture quantitative measurements on tens of thousands of molecules. Therefore, in a time course ‘omics’ experiment molecules are measured for multiple subjects over multiple time points. This results in a large, high-dimensional dataset, which requires computationally efficient approaches for statistical analysis. Moreover, methods need to be able to handle missing values and various levels of noise. We present a novel, robust and powerful framework to analyze time course ‘omics’ data that consists of three stages: quality assessment and filtering, profile modelling, and analysis. The first step consists of removing molecules for which expression or abundance is highly variable over time. The second step models each molecular expression profile in a linear mixed model framework which takes into account subject-specific variability. The best model is selected through a serial model selection approach and results in dimension reduction of the time course data. The final step includes two types of analysis of the modelled trajectories, namely, clustering analysis to identify groups of correlated profiles over time, and differential expression analysis to identify profiles which differ over time and/or between treatment groups. Through simulation studies we demonstrate the high sensitivity and specificity of our approach for differential expression analysis. We then illustrate how our framework can bring novel insights on two time course ‘omics’ studies in breast cancer and kidney rejection. The methods are publicly available, implemented in the R CRAN package lmms.},
	language = {en},
	number = {8},
	urldate = {2020-03-23},
	journal = {PLOS ONE},
	author = {Straube, Jasmin and Gorse, Alain-Dominique and {PROOF Centre of Excellence Team} and Huang, Bevan Emma and Lê Cao, Kim-Anh},
	editor = {Houseman, Eugene Andres},
	month = aug,
	year = {2015},
	pages = {e0134540},
	file = {Straube et al. - 2015 - A Linear Mixed Model Spline Framework for Analysin.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\FBIU8K5X\\Straube et al. - 2015 - A Linear Mixed Model Spline Framework for Analysin.pdf:application/pdf}
}

@article{trefz_effects_2018,
	title = {Effects of humidity, {CO} $_{\textrm{2}}$ and {O} $_{\textrm{2}}$ on real-time quantitation of breath biomarkers by means of {PTR}-{ToF}-{MS}},
	volume = {12},
	issn = {1752-7163},
	url = {https://iopscience.iop.org/article/10.1088/1752-7163/aa9eea},
	doi = {10.1088/1752-7163/aa9eea},
	abstract = {Proton transfer reaction time-of-ﬂight mass spectrometry (PTR-ToF-MS) represents an attractive tool for the real-time analysis of VOC proﬁles in human breath. Quantiﬁcation of breath VOCs by means of direct MS may be affected by the matrix, as human breath not only contains several hundred VOCs at the ppbV–pptV level, but is water saturated and contains percentage levels of CO2. Investigation of breath biomarkers in clinical studies requires quantitative and comparable results. We therefore systematically assessed the effect of humidity, CO2 and O2 on the results of PTR-MS analysis. We investigated more than 20 VOCs, including aldehydes, ketones, aromatic compounds and hydrocarbons with different sample humidity, CO2 and O2 content. The inﬂuence of data processing (e.g. normalization to the H3O+ ion count) was also addressed. An increase of the H3O+ count of about 20\% was observed when the humidity in the sample was increased to breath levels. Large differences regarding the measured VOC intensities were found between the dry and humid samples. Data normalization to the H3O+ or water-clusters could not fully compensate for the humidity-dependent effects. However, as the determination of most VOCs linearly depends on the humidity over the whole investigated range, factor-based correction seems possible. The effects of CO2 were more pronounced in the dry samples than in the humid samples but only had a minor inﬂuence on the results. The same was true for the inﬂuence of O2. For the reliable quantiﬁcation of VOCs in clinical studies and for the standardization of VOC research, well-adapted calibration standards are required for PTR-MS analysis.},
	language = {en},
	number = {2},
	urldate = {2020-04-04},
	journal = {Journal of Breath Research},
	author = {Trefz, Phillip and Schubert, Jochen K and Miekisch, Wolfram},
	month = mar,
	year = {2018},
	pages = {026016},
	file = {Trefz et al. - 2018 - Effects of humidity, CO sub2sub and O sub2.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\UEV8KV3S\\Trefz et al. - 2018 - Effects of humidity, CO sub2sub and O sub2.pdf:application/pdf}
}

@article{sukul_fev_2016,
	title = {{FEV} manoeuvre induced changes in breath {VOC} compositions: an unconventional view on lung function tests},
	volume = {6},
	issn = {2045-2322},
	shorttitle = {{FEV} manoeuvre induced changes in breath {VOC} compositions},
	url = {http://www.nature.com/articles/srep28029},
	doi = {10.1038/srep28029},
	language = {en},
	number = {1},
	urldate = {2020-04-04},
	journal = {Scientific Reports},
	author = {Sukul, Pritam and Schubert, Jochen K. and Oertel, Peter and Kamysek, Svend and Taunk, Khushman and Trefz, Phillip and Miekisch, Wolfram},
	month = jun,
	year = {2016},
	pages = {28029},
	file = {Sukul et al. - 2016 - FEV manoeuvre induced changes in breath VOC compos.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\8C84FU6T\\Sukul et al. - 2016 - FEV manoeuvre induced changes in breath VOC compos.pdf:application/pdf}
}

@article{scheipl_size_2008,
	title = {Size and power of tests for a zero random effect variance or polynomial regression in additive and linear mixed models},
	volume = {52},
	issn = {01679473},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0167947307004306},
	doi = {10.1016/j.csda.2007.10.022},
	abstract = {Several tests for a zero random effect variance in linear mixed models are compared. This testing problem is non-regular because the tested parameter is on the boundary of the parameter space. Size and power of the different tests are investigated in an extensive simulation study that covers a variety of important settings. These include testing for polynomial regression versus a general smooth alternative using penalized splines. Among the test procedures considered, three are based on the restricted likelihood ratio test statistic (RLRT), while six are different extensions of the linear model F-test to the linear mixed model. Four of the tests with unknown null distributions are based on a parametric bootstrap, the other tests rely on approximate or asymptotic distributions. The parametric bootstrap-based tests all have a similar performance. Tests based on approximate F-distributions are usually the least powerful among the tests under consideration. The chi-square mixture approximation for the RLRT is conﬁrmed to be conservative, with corresponding loss in power. A recently developed approximation to the distribution of the RLRT is identiﬁed as a rapid, powerful and reliable alternative to computationally intensive parametric bootstrap procedures. This novel method extends the exact distribution available for models with one random effect to models with several random effects.},
	language = {en},
	number = {7},
	urldate = {2020-07-02},
	journal = {Computational Statistics \& Data Analysis},
	author = {Scheipl, Fabian and Greven, Sonja and Küchenhoff, Helmut},
	month = mar,
	year = {2008},
	pages = {3283--3299},
	file = {Scheipl et al. - 2008 - Size and power of tests for a zero random effect v.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\KPTMF4NW\\Scheipl et al. - 2008 - Size and power of tests for a zero random effect v.pdf:application/pdf}
}

@article{malaskova_proton_2019,
	title = {Proton transfer reaction time-of-flight mass spectrometric measurements of volatile compounds contained in peppermint oil capsules of relevance to real-time pharmacokinetic breath studies},
	volume = {13},
	issn = {1752-7163},
	url = {https://iopscience.iop.org/article/10.1088/1752-7163/ab26e2},
	doi = {10.1088/1752-7163/ab26e2},
	abstract = {With the growing interest in the use of breath volatiles in the health sciences, the lack of standardization for the sampling and analysis of exhaled breath is becoming a major issue leading to an absence of conformity, reproducibility and reliability in spectrometric measurements. Through the creation of a worldwide ‘peppermint consortium’, the International Association of Breath Research has set up a task force to deal with this problem. Pharmacokinetic studies are proposed, and a realtime analytical technique that is being used is proton transfer reaction-time-of-ﬂight-mass spectrometry (PTR-ToF-MS). This paper presents details on how the volatile compounds contained in a peppermint oil capsule, and hence on breath, appear in a PTR-ToF-MS. To aid that study, the key volatiles in the headspace of peppermint oil were ﬁrst identiﬁed using gas chromatography-mass spectrometry, notably: menthol, menthone, 1,8-cineole, menthofuran, limonene, α-pinene and β-pinene. A PTR-ToF-MS analysis of these compounds has been undertaken, divorced from the complexity of the peppermint oil matrix using ‘normal’ and ‘saturated’ humidity drift-tube conditions, with the latter used to mimic breath samples, and over a range of reduced electric ﬁelds. There are no characteristic product ions that can distinguish monoterpenes and 1,8-cineole, and hence, without pre-separation, a combined washout for these volatiles can only be provided. By operating the drift tube above about 130 Td, there are characteristic product ions for menthone, menthofuran and menthol, namely m/z 155.14 (protonated menthone), m/z 151.11 (protonated menthofuran), m/z 139.15 (loss of H2O from protonated menthol) and m/z 83.09 (a fragment ion, C6H1+1, from menthol). These have been used to monitor, with a high speciﬁcity, the temporal proﬁle of these three compounds in breath following the ingestion of a peppermint oil capsule. To aid in the analyses, the proton afﬁnities and gas-phase basicities for the key volatiles investigated have been determined using density functional theory.},
	language = {en},
	number = {4},
	urldate = {2020-07-29},
	journal = {Journal of Breath Research},
	author = {Malásková, Michaela and Henderson, Ben and Chellayah, Prema D and Ruzsanyi, Veronika and Mochalski, Paweł and Cristescu, Simona M and Mayhew, Chris A},
	month = jul,
	year = {2019},
	pages = {046009},
	file = {Malásková et al. - 2019 - Proton transfer reaction time-of-flight mass spect.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\8TGPFWIP\\Malásková et al. - 2019 - Proton transfer reaction time-of-flight mass spect.pdf:application/pdf}
}

@article{rinaudo_biosigner_2016,
	title = {biosigner: {A} {New} {Method} for the {Discovery} of {Significant} {Molecular} {Signatures} from {Omics} {Data}},
	volume = {3},
	issn = {2296-889X},
	shorttitle = {biosigner},
	url = {http://journal.frontiersin.org/Article/10.3389/fmolb.2016.00026/abstract},
	doi = {10.3389/fmolb.2016.00026},
	abstract = {High-throughput technologies such as transcriptomics, proteomics, and metabolomics show great promise for the discovery of biomarkers for diagnosis and prognosis. Selection of the most promising candidates between the initial untargeted step and the subsequent validation phases is critical within the pipeline leading to clinical tests. Several statistical and data mining methods have been described for feature selection: in particular, wrapper approaches iteratively assess the performance of the classiﬁer on distinct subsets of variables. Current wrappers, however, do not estimate the signiﬁcance of the selected features. We therefore developed a new methodology to ﬁnd the smallest feature subset which signiﬁcantly contributes to the model performance, by using a combination of resampling, ranking of variable importance, signiﬁcance assessment by permutation of the feature values in the test subsets, and half-interval search. We wrapped our biosigner algorithm around three reference binary classiﬁers (Partial Least Squares—Discriminant Analysis, Random Forest, and Support Vector Machines) which have been shown to achieve speciﬁc performances depending on the structure of the dataset. By using three real biological and clinical metabolomics and transcriptomics datasets (containing up to 7000 features), complementary signatures were obtained in a few minutes, generally providing higher prediction accuracies than the initial full model. Comparison with alternative feature selection approaches further indicated that our method provides signatures of restricted size and high stability. Finally, by using our methodology to seek metabolites discriminating type 1 from type 2 diabetic patients, several features were selected, including a fragment from the taurochenodeoxycholic bile acid. Our methodology, implemented in the biosigner R/Bioconductor package and Galaxy/Workﬂow4metabolomics module, should be of interest for both experimenters and statisticians to identify robust molecular signatures from large omics datasets in the process of developing new diagnostics.},
	language = {en},
	urldate = {2020-08-06},
	journal = {Frontiers in Molecular Biosciences},
	author = {Rinaudo, Philippe and Boudah, Samia and Junot, Christophe and Thévenot, Etienne A.},
	month = jun,
	year = {2016},
	file = {Rinaudo et al. - 2016 - biosigner A New Method for the Discovery of Signi.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\YWWNCJ7S\\Rinaudo et al. - 2016 - biosigner A New Method for the Discovery of Signi.pdf:application/pdf}
}

@article{weston_feature_nodate,
	title = {Feature {Selection} for {SVMs}},
	abstract = {We introduce a method of feature selection for Support Vector Machines. The method is based upon finding those features which minimize bounds on the leave-one-out error. This search can be efficiently performed via gradient descent. The resulting algorithms are shown to be superior to some standard feature selection algorithms on both toy data and real-life problems of face recognition, pedestrian detection and analyzing DNA microarray data.},
	language = {en},
	author = {Weston, Jason and Mukherjee, Sayan and Chapelle, Olivier and Pontil, Massimiliano and Poggio, Tomaso and Vapnik, Vladimir},
	pages = {7},
	file = {Weston et al. - Feature Selection for SVMs.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\DMVKWNXE\\Weston et al. - Feature Selection for SVMs.pdf:application/pdf}
}

@article{zou_regularization_2005,
	title = {Regularization and variable selection via the elastic net},
	volume = {67},
	issn = {1369-7412, 1467-9868},
	url = {http://doi.wiley.com/10.1111/j.1467-9868.2005.00503.x},
	doi = {10.1111/j.1467-9868.2005.00503.x},
	abstract = {We propose the elastic net, a new regularization and variable selection method. Real world data and a simulation study show that the elastic net often outperforms the lasso, while enjoying a similar sparsity of representation. In addition, the elastic net encourages a grouping effect, where strongly correlated predictors tend to be in or out of the model together. The elastic net is particularly useful when the number of predictors (p) is much bigger than the number of observations (n). By contrast, the lasso is not a very satisfactory variable selection method in the p n case. An algorithm called LARS-EN is proposed for computing elastic net regularization paths efﬁciently, much like algorithm LARS does for the lasso.},
	language = {en},
	number = {2},
	urldate = {2020-08-06},
	journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
	author = {Zou, Hui and Hastie, Trevor},
	month = apr,
	year = {2005},
	pages = {301--320},
	file = {Zou et Hastie - 2005 - Regularization and variable selection via the elas.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\3YZKAY3N\\Zou et Hastie - 2005 - Regularization and variable selection via the elas.pdf:application/pdf}
}

@article{king_dynamic_2010,
	title = {Dynamic profiles of volatile organic compounds in exhaled breath as determined by a coupled {PTR}-{MS}/{GC}-{MS} study},
	volume = {31},
	issn = {0967-3334, 1361-6579},
	url = {https://iopscience.iop.org/article/10.1088/0967-3334/31/9/008},
	doi = {10.1088/0967-3334/31/9/008},
	language = {en},
	number = {9},
	urldate = {2020-10-08},
	journal = {Physiological Measurement},
	author = {King, J and Mochalski, P and Kupferthaler, A and Unterkofler, K and Koc, H and Filipiak, W and Teschl, S and Hinterhuber, H and Amann, A},
	month = sep,
	year = {2010},
	pages = {1169--1184},
	file = {King et al. - 2010 - Dynamic profiles of volatile organic compounds in .pdf:C\:\\Users\\CR258086\\Zotero\\storage\\FW6VD3CZ\\King et al. - 2010 - Dynamic profiles of volatile organic compounds in .pdf:application/pdf}
}

@article{lindinger_unambiguous_2005,
	title = {Unambiguous {Identification} of {Volatile} {Organic} {Compounds} by {Proton}-{Transfer} {Reaction} {Mass} {Spectrometry} {Coupled} with {GC}/{MS}},
	volume = {77},
	issn = {0003-2700, 1520-6882},
	url = {https://pubs.acs.org/doi/10.1021/ac0501240},
	doi = {10.1021/ac0501240},
	language = {en},
	number = {13},
	urldate = {2020-10-08},
	journal = {Analytical Chemistry},
	author = {Lindinger, Christian and Pollien, Philippe and Ali, Santo and Yeretzian, Chahan and Blank, Imre and Märk, Tilmann},
	month = jul,
	year = {2005},
	pages = {4117--4124},
	file = {Lindinger et al. - 2005 - Unambiguous Identification of Volatile Organic Com.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\STYVGXGK\\Lindinger et al. - 2005 - Unambiguous Identification of Volatile Organic Com.pdf:application/pdf}
}

@article{wilson_review_2012,
	title = {Review of {Electronic}-nose {Technologies} and {Algorithms} to {Detect} {Hazardous} {Chemicals} in the {Environment}},
	volume = {1},
	issn = {22120173},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2212017312001028},
	doi = {10.1016/j.protcy.2012.02.101},
	abstract = {Novel mobile electronic-nose (e-nose) devices and algorithms capable of real-time detection of industrial and municipal pollutants, released from point-sources, recently have been developed by scientists worldwide that are useful for monitoring specific environmental-pollutant levels for enforcement and implementation of effective pollution-abatement programs. E-nose devices are ideal instruments for measuring and monitoring carbon and greenhouse-gas emissions due to their sensitivity to a wide diversity of volatile organic compounds (VOCs). A large number of e-nose instrument types, based on a wide diversity of technologies and operational mechanisms, are available to monitor gaseous and particulate pollutants released into the atmosphere, or liquid and dissolved organic pollutants released into municipal and industrial waste-water systems. Some commonly used e-nose technologies include conducting polymers (CP), metal-oxide semiconductor (MOS), quartz crystal microbalance (QCM), and surface acoustic wave (SAW) sensors. Potential pollution-detection applications of e-noses range from atmospheric pollutant (gas-leak) detection of carbon emissions from biofuel production plants and fossil-fuel production sources in the oil and gas industry to VOC-releases from numerous other industries. E-nose technologies are potentially capable of monitoring all phases of industrial manufacturing processes to minimize production of pollutants and maintain efficient, clean production lines. E-nose devices are also useful in designing more environmentallyfriendly, clean technologies for energy production, various industrial processes and product-manufacturing systems. This paper is a review of recent novel electronic-nose systems and algorithms, developed over the past decade, that have potential applications for detecting specific types of harmful VOC pollutants in the environment to meet carbon-capture and emission-reduction targets of worldwide environmental protection agencies.},
	language = {en},
	urldate = {2020-10-08},
	journal = {Procedia Technology},
	author = {Wilson, Alphus Dan},
	year = {2012},
	pages = {453--463},
	file = {Wilson - 2012 - Review of Electronic-nose Technologies and Algorit.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\QQFHKK56\\Wilson - 2012 - Review of Electronic-nose Technologies and Algorit.pdf:application/pdf}
}

@article{saidi_exhaled_2018,
	title = {Exhaled breath analysis using electronic nose and gas chromatography–mass spectrometry for non-invasive diagnosis of chronic kidney disease, diabetes mellitus and healthy subjects},
	volume = {257},
	issn = {09254005},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0925400517320920},
	doi = {10.1016/j.snb.2017.10.178},
	abstract = {Breath Volatile Organic Compounds (VOC’s) analysis is a non-invasive tool to assess information about health status. This study aims to investigate exhaled breath of Chronic Kidney Disease (CKD), Diabetes Mellitus (DM) and Healthy Subjects (HS), using electronic nose (e-nose) and Gas Chromatography Quadrupole Time-Of-Flight Mass spectrometry (GC/Q-TOF-MS). Breath samples were collected from 44 volunteers containing 14 females and 30 males. Urine samples were also collected to measure Creatinine Level (CL) by UV–vis Spectrophotometry as reference method. GC/Q-TOF-MS was used to identify volatile organic compounds that were detected in the exhaled breath of CKD, DM, and healthy subjects at different CL concentrations. The e-nose dataset was treated with Principal Component Analysis (PCA), Support Vector Machines (SVMs), Hierarchical Cluster Analysis (HCA) and Partial Least Squares-regression (PLSregression). PLS model revealed a relationship between breath and urinary CL. The presented results show that e-nose based on chemical gas sensors in combination with pattern recognition methods could constitute the basis of inexpensive and non-invasive diagnosis to distinguish between breath of CKD, DM patients and healthy controls based on breath VOC’s analysis.},
	language = {en},
	urldate = {2020-10-08},
	journal = {Sensors and Actuators B: Chemical},
	author = {Saidi, Tarik and Zaim, Omar and Moufid, Mohammed and El Bari, Nezha and Ionescu, Radu and Bouchikhi, Benachir},
	month = mar,
	year = {2018},
	pages = {178--188},
	file = {Saidi et al. - 2018 - Exhaled breath analysis using electronic nose and .pdf:C\:\\Users\\CR258086\\Zotero\\storage\\C3HWAEWH\\Saidi et al. - 2018 - Exhaled breath analysis using electronic nose and .pdf:application/pdf}
}

@article{hansel_proton_1995-1,
	title = {Proton transfer reaction mass spectrometry: on-line trace gas analysis at the ppb level},
	volume = {149-150},
	issn = {01681176},
	shorttitle = {Proton transfer reaction mass spectrometry},
	url = {https://linkinghub.elsevier.com/retrieve/pii/016811769504294U},
	doi = {10.1016/0168-1176(95)04294-U},
	abstract = {A system for trace gas analysis using proton transfer reaction mass spectrometry (PTR-MS) has been developed which allows for on-line measurements of components with concentrations as low as 1 ppb. The method is based on reactions of HsO+ ions, which perform non-dissociative proton transfer to most of the common organic trace constituents but do not react with any of the components present in clean air. Examples of analysis of breath taken from smokers and non-smokers as well as from patients suffering from cirrhosis of the liver, and of air in buildings as well as of ambient air taken at a road crossing demonstrate the wide range of applicability of this method. An enhanced level of acetonitrile in the breath is a most suitable indicator that a person is a smoker. Enhanced levels of propanol strongly indicate that a person has a severe liver deficiency.},
	language = {en},
	urldate = {2020-10-14},
	journal = {International Journal of Mass Spectrometry and Ion Processes},
	author = {Hansel, A. and Jordan, A. and Holzinger, R. and Prazeller, P. and Vogel, W. and Lindinger, W.},
	month = nov,
	year = {1995},
	pages = {609--619},
	file = {Hansel et al. - 1995 - Proton transfer reaction mass spectrometry on-lin.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\JTFV9QLR\\Hansel et al. - 1995 - Proton transfer reaction mass spectrometry on-lin.pdf:application/pdf}
}

@article{smith_jamss_2015,
	title = {{JAMSS}: proteomics mass spectrometry simulation in {Java}},
	volume = {31},
	issn = {1367-4803, 1460-2059},
	shorttitle = {{JAMSS}},
	url = {https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btu729},
	doi = {10.1093/bioinformatics/btu729},
	abstract = {Summary: Countless proteomics data processing algorithms have been proposed, yet few have been critically evaluated due to lack of labeled data (data with known identities and quantities). Although labeling techniques exist, they are limited in terms of conﬁdence and accuracy. In silico simulators have recently been used to create complex data with known identities and quantities. We propose Java Mass Spectrometry Simulator (JAMSS): a fast, self-contained in silico simulator capable of generating simulated MS and LC-MS runs while providing meta information on the provenance of each generated signal. JAMSS improves upon previous in silico simulators in terms of its ease to install, minimal parameters, graphical user interface, multithreading capability, retention time shift model and reproducibility.},
	language = {en},
	number = {5},
	urldate = {2020-10-27},
	journal = {Bioinformatics},
	author = {Smith, R. and Prince, J. T.},
	month = mar,
	year = {2015},
	pages = {791--793},
	file = {Smith et Prince - 2015 - JAMSS proteomics mass spectrometry simulation in .pdf:C\:\\Users\\CR258086\\Zotero\\storage\\J5RBP3VE\\Smith et Prince - 2015 - JAMSS proteomics mass spectrometry simulation in .pdf:application/pdf}
}

@article{kim_optimal_nodate,
	title = {An optimal peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry using mixture similarity measure},
	abstract = {Motivation: Comprehensive two-dimensional gas chromatography mass spectrometry (GC × GC–MS) brings much increased separation capacity, chemical selectivity and sensitivity for metabolomics and provides more accurate information about metabolite retention times and mass spectra. However, there is always a shift of retention times in the two columns that makes it difﬁcult to compare metabolic proﬁles obtained from multiple samples exposed to different experimental conditions.},
	language = {en},
	author = {Kim, Seongho and Fang, Aiqin and Wang, Bing and Jeong, Jaesik and Zhang, Xiang},
	pages = {7},
	file = {Kim et al. - An optimal peak alignment for comprehensive two-di.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\KC36EDFV\\Kim et al. - An optimal peak alignment for comprehensive two-di.pdf:application/pdf}
}

@article{unser_b-spline_1993,
	title = {B-spline signal processing. {I}. {Theory}},
	volume = {41},
	issn = {1053587X},
	url = {http://ieeexplore.ieee.org/document/193220/},
	doi = {10.1109/78.193220},
	language = {en},
	number = {2},
	urldate = {2020-10-30},
	journal = {IEEE Transactions on Signal Processing},
	author = {Unser, M. and Aldroubi, A. and Eden, M.},
	month = feb,
	year = {1993},
	pages = {821--833},
	file = {Unser et al. - 1993 - B-spline signal processing. I. Theory.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\ANHJ7I7P\\Unser et al. - 1993 - B-spline signal processing. I. Theory.pdf:application/pdf}
}

@article{unser_splines_1999,
	title = {Splines: a perfect fit for signal and image processing},
	volume = {16},
	issn = {10535888},
	shorttitle = {Splines},
	url = {http://ieeexplore.ieee.org/document/799930/},
	doi = {10.1109/79.799930},
	language = {en},
	number = {6},
	urldate = {2020-10-30},
	journal = {IEEE Signal Processing Magazine},
	author = {Unser, M.},
	month = nov,
	year = {1999},
	pages = {22--38},
	file = {Unser - 1999 - Splines a perfect fit for signal and image proces.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\TFF9AXSZ\\Unser - 1999 - Splines a perfect fit for signal and image proces.pdf:application/pdf}
}

@inproceedings{blair_optimal_2008,
	address = {Victoria, BC, Canada},
	title = {Optimal knot selection for least-squares fitting of noisy data with spline functions},
	isbn = {978-1-4244-1540-3},
	url = {http://ieeexplore.ieee.org/document/4546998/},
	doi = {10.1109/IMTC.2008.4546998},
	abstract = {An automatic data-smoothing algorithm for data from digital oscilloscopes is described. The algorithm adjusts the bandwidth of the filtering as a function of time to provide minimum mean squared error at each time. It produces an estimate of the root-mean-square error as a function of time and does so without any statistical assumptions about the unknown signal. The algorithm is based on least-squares fitting to the data ofcubic spline functions.},
	language = {en},
	urldate = {2020-10-30},
	booktitle = {2008 {IEEE} {Instrumentation} and {Measurement} {Technology} {Conference}},
	publisher = {IEEE},
	author = {Blair, Jerome},
	month = may,
	year = {2008},
	pages = {27--32},
	file = {Blair - 2008 - Optimal knot selection for least-squares fitting o.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\GD3EL8I7\\Blair - 2008 - Optimal knot selection for least-squares fitting o.pdf:application/pdf}
}

@inproceedings{bharati_image_2011,
	address = {Hyderabad, India},
	title = {Image reconstruction using cubic {B}-{Spline} interpolation},
	isbn = {978-1-4577-1109-1 978-1-4577-1110-7 978-1-4577-1108-4},
	url = {http://ieeexplore.ieee.org/document/6139378/},
	doi = {10.1109/INDCON.2011.6139378},
	abstract = {As the development and use of multimedia technology in different and varied fields has led to an explosion in its use in all environments, in medical, military, environmental, surveillance as well as industrial and quality control applications. In many of these applications a compression step is necessary with the inevitable loss of quality information, for the sake of saving a little more bandwidth or storage space. While doing compression, we generally discard some pixels or frame during encoding and even upon decoding/decompression the exact data is not regenerated therefore the final image is not exactly the same as the original image. Thus to incorporate the compression losses, reconstruction using interpolation technique have been applied on the compressed image such that this can predict the discarded pixels or the missing pixels from the image. The proposed algorithm uses cubic B-Spline interpolation technique for reconstruction, exhibits significant improvement in reconstructed image quality.},
	language = {en},
	urldate = {2020-10-30},
	booktitle = {2011 {Annual} {IEEE} {India} {Conference}},
	publisher = {IEEE},
	author = {Bharati, Nilashma and Khosla, Arun and Sood, Neetu},
	month = dec,
	year = {2011},
	pages = {1--5},
	file = {Bharati et al. - 2011 - Image reconstruction using cubic B-Spline interpol.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\BSLYN5L8\\Bharati et al. - 2011 - Image reconstruction using cubic B-Spline interpol.pdf:application/pdf}
}

@article{kai-yu_application_nodate,
	title = {The application of {B}-spline based interpolation in real-time image enlarging processing},
	abstract = {Efficient algorithms for the continuous representation of a discrete signal in terms of B-splines and for interpolative signal reconstruction have been proposed in this paper. It analyzes the relationship between the degree of the spline and the quality of the interpolation. By taking the z-transforms of the sampled B-spline functions, a fast interpolation algorithm based on digital filters of IIR and FIR is proposed, which is quite suitable for hardware realization with its ideal processing result and high-speed computing. Through the example of image enlargement, the application of cubic B-spline based interpolation in image processing is investigated. It designs a fast and high-quality image enlargement and display system based on FPGA. It is proved in the experiment to be qualified for the real-time image processing.},
	language = {en},
	author = {Kai-yu, Li and Wen-dong, Wang and Kai-wen, Zheng and Wen-bo, Liu and Gui-li, Xu},
	pages = {5},
	file = {Kai-yu et al. - The application of B-spline based interpolation in.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\FMJZPIKC\\Kai-yu et al. - The application of B-spline based interpolation in.pdf:application/pdf}
}

@article{sidiropoulos_tensor_2017,
	title = {Tensor {Decomposition} for {Signal} {Processing} and {Machine} {Learning}},
	volume = {65},
	issn = {1053-587X, 1941-0476},
	url = {http://ieeexplore.ieee.org/document/7891546/},
	doi = {10.1109/TSP.2017.2690524},
	abstract = {Tensors or multiway arrays are functions of three or more indices (i, j, k, . . . )—similar to matrices (two-way arrays), which are functions of two indices (r, c) for (row, column). Tensors have a rich history, stretching over almost a century, and touching upon numerous disciplines; but they have only recently become ubiquitous in signal and data analytics at the conﬂuence of signal processing, statistics, data mining, and machine learning. This overview article aims to provide a good starting point for researchers and practitioners interested in learning about and working with tensors. As such, it focuses on fundamentals and motivation (using various application examples), aiming to strike an appropriate balance of breadth and depth that will enable someone having taken ﬁrst graduate courses in matrix algebra and probability to get started doing research and/or developing tensor algorithms and software. Some background in applied optimization is useful but not strictly required. The material covered includes tensor rank and rank decomposition; basic tensor factorization models and their relationships and properties (including fairly good coverage of identiﬁability); broad coverage of algorithms ranging from alternating optimization to stochastic gradient; statistical performance analysis; and applications ranging from source separation to collaborative ﬁltering, mixture and topic modeling, classiﬁcation, and multilinear subspace learning.},
	language = {en},
	number = {13},
	urldate = {2020-10-30},
	journal = {IEEE Transactions on Signal Processing},
	author = {Sidiropoulos, Nicholas D. and De Lathauwer, Lieven and Fu, Xiao and Huang, Kejun and Papalexakis, Evangelos E. and Faloutsos, Christos},
	month = jul,
	year = {2017},
	pages = {3551--3582},
	file = {Sidiropoulos et al. - 2017 - Tensor Decomposition for Signal Processing and Mac.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\CLUMEKKB\\Sidiropoulos et al. - 2017 - Tensor Decomposition for Signal Processing and Mac.pdf:application/pdf}
}

@article{takeda_kernel_2007,
	title = {Kernel {Regression} for {Image} {Processing} and {Reconstruction}},
	volume = {16},
	issn = {1057-7149},
	url = {http://ieeexplore.ieee.org/document/4060955/},
	doi = {10.1109/TIP.2006.888330},
	abstract = {In this paper, we make contact with the ﬁeld of nonparametric statistics and present a development and generalization of tools and results for use in image processing and reconstruction. In particular, we adapt and expand kernel regression ideas for use in image denoising, upscaling, interpolation, fusion, and more. Furthermore, we establish key relationships with some popular existing methods and show how several of these algorithms, including the recently popularized bilateral ﬁlter, are special cases of the proposed framework. The resulting algorithms and analyses are amply illustrated with practical examples.},
	language = {en},
	number = {2},
	urldate = {2020-10-30},
	journal = {IEEE Transactions on Image Processing},
	author = {Takeda, Hiroyuki and Farsiu, Sina and Milanfar, Peyman},
	month = feb,
	year = {2007},
	pages = {349--366},
	file = {Takeda et al. - 2007 - Kernel Regression for Image Processing and Reconst.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\G4V68YIB\\Takeda et al. - 2007 - Kernel Regression for Image Processing and Reconst.pdf:application/pdf}
}

@article{unser_splines_nodate,
	title = {Splines: a perfect fit for medical imaging},
	volume = {4684},
	abstract = {Splines, which were invented by Schoenberg more than fifty years ago, constitute an elegant framework for dealing with interpolation and discretization problems. They are widely used in computer-aided design and computer graphics, but have been neglected in medical imaging applications, mostly as a consequence of what one may call the "bad press" phenomenon. Thanks to some recent research efforts in signal processing and wavelet-related techniques, the virtues of splines have been revived in our community. There is now compelling evidence (several independent studies) that splines offer the best cost-performance tradeoff among available interpolation methods. In this presentation, we will argue that the spline representation is ideally suited for all processing tasks that require a continuous model of signals or images. We will show that most forms of spline fitting (interpolation, least squares approximation, smoothing splines) can be performed most efficiently using recursive digital filters. We will also have a look at their multiresolution properties which make them prime candidates for constructing wavelet bases and computing image pyramids. Typical application areas where these techniques can be useful are: image reconstruction from projection data, sampling grid conversion, geometric correction, visualization, rigid or elastic image registration, and feature extraction including edge detection and active contour models.},
	language = {en},
	author = {Unser, Michael},
	pages = {13},
	file = {225.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\IM8P48DX\\225.pdf:application/pdf}
}

@article{jager_confounding_2008,
	title = {Confounding: {What} it is and how to deal with it},
	volume = {73},
	issn = {00852538},
	shorttitle = {Confounding},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0085253815529748},
	doi = {10.1038/sj.ki.5002650},
	language = {en},
	number = {3},
	urldate = {2020-11-03},
	journal = {Kidney International},
	author = {Jager, K.J. and Zoccali, C. and MacLeod, A. and Dekker, F.W.},
	month = feb,
	year = {2008},
	pages = {256--260},
	file = {Jager et al. - 2008 - Confounding What it is and how to deal with it.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\ALJU65CD\\Jager et al. - 2008 - Confounding What it is and how to deal with it.pdf:application/pdf}
}

@article{li_mcee_2018,
	title = {{MCEE}: a data preprocessing approach for metabolic confounding effect elimination},
	volume = {410},
	issn = {1618-2642, 1618-2650},
	shorttitle = {{MCEE}},
	url = {http://link.springer.com/10.1007/s00216-018-0947-4},
	doi = {10.1007/s00216-018-0947-4},
	abstract = {It is well recognized that physiological and environmental factors such as race, age, gender, and diurnal cycles often have a definite influence on metabolic results that statistically manifests as confounding variables. Currently, removal or controlling of confounding effects relies heavily on experimental design. There are no available data processing techniques focusing on the compensation of their effects. We therefore proposed a new method, Metabolic confounding effect elimination (MCEE), to remove the influence of specified confounding factors and make the data more accurate. The method consists of three steps: metabolites grouping, confounder-related metabolites selection, and metabolites modification. Its effectiveness and advantages were evaluated comprehensively by several simulated models and real datasets, and were compared with two typical methods, the principal component analysis (PCA)- and the direct orthogonal signal correction (DOSC)-based methods. MCEE is simple, effective, and safe, and is independent of sample number, association degree, and missing value. Hence, it may serve as a good complement to existing metabolomics data preprocessing methods and aid in better understanding the metabolic and biological status of interest.},
	language = {en},
	number = {11},
	urldate = {2020-11-03},
	journal = {Analytical and Bioanalytical Chemistry},
	author = {Li, Yitao and Li, Mengci and Jia, Wei and Ni, Yan and Chen, Tianlu},
	month = apr,
	year = {2018},
	pages = {2689--2699},
	file = {Li et al. - 2018 - MCEE a data preprocessing approach for metabolic .pdf:C\:\\Users\\CR258086\\Zotero\\storage\\CT4MRLTN\\Li et al. - 2018 - MCEE a data preprocessing approach for metabolic .pdf:application/pdf}
}

@article{christenfeld_risk_2004,
	title = {Risk {Factors}, {Confounding}, and the {Illusion} of {Statistical} {Control}:},
	volume = {66},
	issn = {0033-3174},
	shorttitle = {Risk {Factors}, {Confounding}, and the {Illusion} of {Statistical} {Control}},
	url = {http://journals.lww.com/00006842-200411000-00011},
	doi = {10.1097/01.psy.0000140008.70959.41},
	abstract = {When experimental designs are premature, impractical, or impossible, researchers must rely on statistical methods to adjust for potentially confounding effects. Such procedures, however, are quite fallible. We examine several errors that often follow the use of statistical adjustment. The first is inferring a factor is causal because it predicts an outcome even after “statistical control” for other factors. This inference is fallacious when (as usual) such control involves removing the linear contribution of imperfectly measured variables, or when some confounders remain unmeasured. The converse fallacy is inferring a factor is not causally important because its association with the outcome is attenuated or eliminated by the inclusion of covariates in the adjustment process. This attenuation may only reflect that the covariates treated as confounders are actually mediators (intermediates) and critical to the causal chain from the study factor to the study outcome. Other problems arise due to mismeasurement of the study factor or outcome, or because these study variables are only proxies for underlying constructs. Statistical adjustment serves a useful function, but it cannot transform observational studies into natural experiments, and involves far more subjective judgment than many users realize. Key words: confounds, risk factors, statistical control, mediators, covariates.},
	language = {en},
	number = {6},
	urldate = {2020-11-03},
	journal = {Psychosomatic Medicine},
	author = {Christenfeld, Nicholas J. S. and Sloan, Richard P. and Carroll, Douglas and Greenland, Sander},
	month = nov,
	year = {2004},
	pages = {868--875},
	file = {Christenfeld et al. - 2004 - Risk Factors, Confounding, and the Illusion of Sta.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\RCMXB8JU\\Christenfeld et al. - 2004 - Risk Factors, Confounding, and the Illusion of Sta.pdf:application/pdf}
}

@article{pourhoseingholi_how_nodate,
	title = {How to control confounding effects by statistical analysis},
	abstract = {A Confounder is a variable whose presence affects the variables being studied so that the results do not reflect the actual relationship. There are various ways to exclude or control confounding variables including Randomization, Restriction and Matching. But all these methods are applicable at the time of study design. When experimental designs are premature, impractical, or impossible, researchers must rely on statistical methods to adjust for potentially confounding effects. These Statistical models (especially regression models) are flexible to eliminate the effects of confounders.},
	language = {en},
	author = {Pourhoseingholi, Mohamad Amin and Baghestani, Ahmad Reza and Vahedi, Mohsen},
	pages = {5},
	file = {Pourhoseingholi et al. - How to control confounding effects by statistical .pdf:C\:\\Users\\CR258086\\Zotero\\storage\\PS367I7E\\Pourhoseingholi et al. - How to control confounding effects by statistical .pdf:application/pdf}
}

@article{bruderer_-line_2019,
	title = {On-{Line} {Analysis} of {Exhaled} {Breath}: \textit{{Focus} {Review}}},
	volume = {119},
	issn = {0009-2665, 1520-6890},
	shorttitle = {On-{Line} {Analysis} of {Exhaled} {Breath}},
	url = {https://pubs.acs.org/doi/10.1021/acs.chemrev.9b00005},
	doi = {10.1021/acs.chemrev.9b00005},
	abstract = {On-line analysis of exhaled breath oﬀers insight into a person’s metabolism without the need for sample preparation or sample collection. Due to its noninvasive nature and the possibility to sample continuously, the analysis of breath has great clinical potential. The unique features of this technology make it an attractive candidate for applications in medicine, beyond the task of diagnosis. We review the current methodologies for on-line breath analysis, discuss current and future applications, and critically evaluate challenges and pitfalls such as the need for standardization. Special emphasis is given to the use of the technology in diagnosing respiratory diseases, potential niche applications, and the promise of breath analysis for personalized medicine. The analytical methodologies used range from very small and low-cost chemical sensors, which are ideal for continuous monitoring of disease status, to optical spectroscopy and state-of-the-art, high-resolution mass spectrometry. The latter can be utilized for untargeted analysis of exhaled breath, with the capability to identify hitherto unknown molecules. The interpretation of the resulting big data sets is complex and often constrained due to a limited number of participants. Even larger data sets will be needed for assessing reproducibility and for validation of biomarker candidates. In addition, molecular structures and quantiﬁcation of compounds are generally not easily available from on-line measurements and require complementary measurements, for example, a separation method coupled to mass spectrometry. Furthermore, a lack of standardization still hampers the application of the technique to screen larger cohorts of patients. This review summarizes the present status and continuous improvements of the principal on-line breath analysis methods and evaluates obstacles for their wider application.},
	language = {en},
	number = {19},
	urldate = {2020-11-05},
	journal = {Chemical Reviews},
	author = {Bruderer, Tobias and Gaisl, Thomas and Gaugg, Martin T. and Nowak, Nora and Streckenbach, Bettina and Müller, Simona and Moeller, Alexander and Kohler, Malcolm and Zenobi, Renato},
	month = oct,
	year = {2019},
	pages = {10803--10828},
	file = {Bruderer et al. - 2019 - On-Line Analysis of Exhaled Breath Focus Revie.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\EVX7ED6M\\Bruderer et al. - 2019 - On-Line Analysis of Exhaled Breath Focus Revie.pdf:application/pdf}
}

@article{katajamaa_data_2007,
	title = {Data processing for mass spectrometry-based metabolomics},
	volume = {1158},
	issn = {00219673},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0021967307006966},
	doi = {10.1016/j.chroma.2007.04.021},
	abstract = {Modern analytical technologies afford comprehensive and quantitative investigation of a multitude of different metabolites. Typical metabolomic experiments can therefore produce large amounts of data. Handling such complex datasets is an important step that has big impact on extent and quality at which the metabolite identiﬁcation and quantiﬁcation can be made, and thus on the ultimate biological interpretation of results. Increasing interest in metabolomics thus led to resurgence of interest in related data processing. A wide variety of methods and software tools have been developed for metabolomics during recent years, and this trend is likely to continue. In this paper we overview the key steps of metabolomic data processing and focus on reviewing recent literature related to this topic, particularly on methods for handling data from liquid chromatography mass spectrometry (LC–MS) experiments.},
	language = {en},
	number = {1-2},
	urldate = {2020-11-05},
	journal = {Journal of Chromatography A},
	author = {Katajamaa, Mikko and Orešič, Matej},
	month = jul,
	year = {2007},
	pages = {318--328},
	file = {Katajamaa et Orešič - 2007 - Data processing for mass spectrometry-based metabo.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\K85Y3Q39\\Katajamaa et Orešič - 2007 - Data processing for mass spectrometry-based metabo.pdf:application/pdf}
}

@article{bielow_mssimulator_2011,
	title = {{MSSimulator}: {Simulation} of {Mass} {Spectrometry} {Data}},
	volume = {10},
	issn = {1535-3893, 1535-3907},
	shorttitle = {{MSSimulator}},
	url = {https://pubs.acs.org/doi/abs/10.1021/pr200155f},
	doi = {10.1021/pr200155f},
	abstract = {Mass spectrometry coupled to liquid chromatography (LCÀMS and LCÀMS/MS) is commonly used to analyze the protein content of biological samples in large scale studies, enabling quantitation and identiﬁcation of proteins and peptides using a wide range of experimental protocols, algorithms, and statistical models to analyze the data. Currently it is diﬃcult to compare the plethora of algorithms for these tasks. So far, curated benchmark data exists for peptide identiﬁcation algorithms but data that represents a ground truth for the evaluation of LCÀMS data is limited. Hence there have been attempts to simulate such data in a controlled fashion to evaluate and compare algorithms. We present MSSimulator, a simulation software for LCÀMS and LCÀMS/MS experiments. Starting from a list of proteins from a FASTA ﬁle, the simulation will perform in-silico digestion, retention time prediction, ionization ﬁltering, and raw signal simulation (including MS/MS), while providing many options to change the properties of the resulting data like elution proﬁle shape, resolution and sampling rate. Several protocols for SILAC, iTRAQ or MSE are available, in addition to the usual label-free approach, making MSSimulator the most comprehensive simulator for LCÀMS and LCÀMS/MS data.},
	language = {en},
	number = {7},
	urldate = {2020-11-09},
	journal = {Journal of Proteome Research},
	author = {Bielow, Chris and Aiche, Stephan and Andreotti, Sandro and Reinert, Knut},
	month = jul,
	year = {2011},
	pages = {2922--2929},
	file = {pr200155f.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\D2992JM2\\pr200155f.pdf:application/pdf}
}

@article{du_noise_nodate,
	title = {A noise model for mass spectrometry based proteomics},
	abstract = {Motivation: Mass spectrometry data are subjected to considerable noise. Good noise models are required for proper detection and quantification of peptides. We have characterized noise in both quadrupole time-of-flight (Q-TOF) and ion trap data, and have constructed models for the noise.},
	language = {en},
	author = {Du, Peicheng and Stolovitzky, Gustavo and Horvatovich, Peter and Bischoff, Rainer and Lim, Jihyeon and Suits, Frank},
	pages = {8},
	file = {btn078.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\PR8GWREV\\btn078.pdf:application/pdf}
}

@article{coombes_understanding_nodate,
	title = {Understanding the characteristics of mass spectrometry data through the use of simulation},
	abstract = {Background: Mass spectrometry is actively being used to discover disease-related proteomic patterns in complex mixtures of proteins derived from tissue samples or from easily obtained biological ﬂuids. The potential importance of these clinical applications has made the development of better methods for processing and analyzing the data an active area of research. It is, however, difﬁcult to determine which methods are better without knowing the true biochemical composition of the samples used in the experiments.
Methods: We developed a mathematical model based on the physics of a simple MALDI-TOF mass spectrometer with time-lag focusing. Using this model, we implemented a statistical simulation of mass spectra. We used the simulation to explore some of the basicoperating characteristics of MALDI or SELDI instruments.
Results: The simulation reproduced several characteristics of actual instruments. We found that the relative mass error is affected bythe time discretization of the detector (about 0.01\%) and the spread of initial velocities (about 0.1\%). The accuracy of calibration based on external standards decays rapidly outside the range spanned by the calibrants. Natural isotope distributions play a major role inbroadening peaks associated with individual proteins. The area of a peak is a more accurate measure of its size than the height.
Conclusions: The model described here is capable of simulating realistic mass spectra. The simulation should become a useful tool forgenerating spectra where the true inputs are known, allowing researchers to evaluate the performance of new methods for processing and analyzing mass spectra.},
	language = {en},
	journal = {Cancer Informatics},
	author = {Coombes, Kevin R and Koomen, John M and Baggerly, Keith A and Morris, Jeffrey S and Kobayashi, Ryuji},
	pages = {12},
	file = {Coombes et al. - Understanding the characteristics of mass spectrom.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\EDQV33UU\\Coombes et al. - Understanding the characteristics of mass spectrom.pdf:application/pdf}
}

@article{morris_feature_2005,
	title = {Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum},
	volume = {21},
	issn = {1367-4803, 1460-2059},
	url = {https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/bti254},
	doi = {10.1093/bioinformatics/bti254},
	abstract = {Motivation: Mass spectrometry yields complex functional data for which the features of scientiﬁc interest are peaks. A common twostep approach to analyzing these data involves ﬁrst extracting and quantifying the peaks, then analyzing the resulting matrix of peak quantiﬁcations. Feature extraction and quantiﬁcation involves a number of interrelated steps. It is important to perform these steps well, since subsequent analyses condition on these determinations. Also, it is difﬁcult to compare the performance of competing methods for analyzing mass spectrometry data since the true expression levels of the proteins in the population are generally not known.},
	language = {en},
	number = {9},
	urldate = {2020-11-10},
	journal = {Bioinformatics},
	author = {Morris, J. S. and Coombes, K. R. and Koomen, J. and Baggerly, K. A. and Kobayashi, R.},
	month = may,
	year = {2005},
	pages = {1764--1775},
	file = {Morris et al. - 2005 - Feature extraction and quantification for mass spe.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\PSA85M7B\\Morris et al. - 2005 - Feature extraction and quantification for mass spe.pdf:application/pdf}
}

@article{gundlach-graham_monte_2018,
	title = {Monte {Carlo} {Simulation} of {Low}-{Count} {Signals} in {Time}-of-{Flight} {Mass} {Spectrometry} and {Its} {Application} to {Single}-{Particle} {Detection}},
	abstract = {Many modern time-of-ﬂight mass spectrometry (TOFMS) instruments use fast analog-to-digital conversion (ADC) with high-speed digitizers to record mass spectra with extended dynamic range (compared to time-to-digital conversion). The extended dynamic range oﬀered by ADC detection is critical for accurate measurement of transient events. However, the use of ADC also increases the variance of the measurements by sampling the gain statistics of electron multipliers (EMs) used for detection. The inﬂuence of gain statistics on the shape of TOF signal distributions is especially pronounced at low count rates and is a major contributor to measurement variance. Here, we use Monte Carlo methods to simulate low-ion-count TOFMS signals as a function of Poisson statistics and the measured pulse-height distribution (PHD) of the EM detection system. We ﬁnd that a compound Poisson distribution calculated via Monte Carlo simulation eﬀectively describes the shape of measured TOFMS signals. Additionally, we apply Monte Carlo simulation results to single-particle inductively coupled plasma (sp-ICP) TOFMS analysis. We demonstrate that subtraction of modeled TOFMS signals can be used to quantitatively uncover particle-signal distributions buried beneath dissolved-signal backgrounds. On the basis of simulated signal distributions, we also calculate new critical values (LC) that are used as decision thresholds for the detection of discrete particles. This new detection criterion better accounts for the shape of dissolved signal distributions and therefore provides more robust identiﬁcation of single particles with ICPTOFMS.},
	language = {en},
	journal = {Anal. Chem.},
	author = {Gundlach-Graham, Alexander and Hendriks, Lyndsey and Mehrabi, Kamyar and Gu, Detlef},
	year = {2018},
	pages = {9},
	file = {acs.analchem.8b01551.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\IX3TDP3H\\acs.analchem.8b01551.pdf:application/pdf}
}

@article{wijetunge_new_2015,
	title = {A new peak detection algorithm for {MALDI} mass spectrometry data based on a modified {Asymmetric} {Pseudo}-{Voigt} model},
	volume = {16},
	issn = {1471-2164},
	url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-16-S12-S12},
	doi = {10.1186/1471-2164-16-S12-S12},
	abstract = {Background: Mass Spectrometry (MS) is a ubiquitous analytical tool in biological research and is used to measure the mass-to-charge ratio of bio-molecules. Peak detection is the essential first step in MS data analysis. Precise estimation of peak parameters such as peak summit location and peak area are critical to identify underlying biomolecules and to estimate their abundances accurately. We propose a new method to detect and quantify peaks in mass spectra. It uses dual-tree complex wavelet transformation along with Stein’s unbiased risk estimator for spectra smoothing. Then, a new method, based on the modified Asymmetric Pseudo-Voigt (mAPV) model and hierarchical particle swarm optimization, is used for peak parameter estimation.
Results: Using simulated data, we demonstrated the benefit of using the mAPV model over Gaussian, Lorentz and Bi-Gaussian functions for MS peak modelling. The proposed mAPV model achieved the best fitting accuracy for asymmetric peaks, with lower percentage errors in peak summit location estimation, which were 0.17\% to 4.46\% less than that of the other models. It also outperformed the other models in peak area estimation, delivering lower percentage errors, which were about 0.7\% less than its closest competitor - the Bi-Gaussian model. In addition, using data generated from a MALDI-TOF computer model, we showed that the proposed overall algorithm outperformed the existing methods mainly in terms of sensitivity. It achieved a sensitivity of 85\%, compared to 77\% and 71\% of the two benchmark algorithms, continuous wavelet transformation based method and Cromwell respectively.
Conclusions: The proposed algorithm is particularly useful for peak detection and parameter estimation in MS data with overlapping peak distributions and asymmetric peaks. The algorithm is implemented using MATLAB and the source code is freely available at http://mapv.sourceforge.net.},
	language = {en},
	number = {S12},
	urldate = {2020-11-12},
	journal = {BMC Genomics},
	author = {Wijetunge, Chalini D and Saeed, Isaam and Boughton, Berin A and Roessner, Ute and Halgamuge, Saman K},
	month = dec,
	year = {2015},
	pages = {S12},
	file = {Wijetunge et al. - 2015 - A new peak detection algorithm for MALDI mass spec.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\HKS3IQ46\\Wijetunge et al. - 2015 - A new peak detection algorithm for MALDI mass spec.pdf:application/pdf}
}

@article{yu_quantification_2010,
	title = {Quantification and deconvolution of asymmetric {LC}-{MS} peaks using the bi-{Gaussian} mixture model and statistical model selection},
	volume = {11},
	issn = {1471-2105},
	url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-559},
	doi = {10.1186/1471-2105-11-559},
	abstract = {Background: Liquid chromatography-mass spectrometry (LC-MS) is one of the major techniques for the quantification of metabolites in complex biological samples. Peak modeling is one of the key components in LC-MS data pre-processing.
Results: To quantify asymmetric peaks with high noise level, we developed an estimation procedure using the bi-Gaussian function. In addition, to accurately quantify partially overlapping peaks, we developed a deconvolution method using the bi-Gaussian mixture model combined with statistical model selection.
Conclusions: Using extensive simulations and real data, we demonstrated the advantage of the bi-Gaussian mixture model over the Gaussian mixture model and the method of kernel smoothing combined with signal summation in peak quantification and deconvolution. The method is implemented in the R package apLCMS: http://www.sph.emory.edu/apLCMS/.},
	language = {en},
	number = {1},
	urldate = {2020-11-12},
	journal = {BMC Bioinformatics},
	author = {Yu, Tianwei and Peng, Hesen},
	month = dec,
	year = {2010},
	pages = {559},
	file = {Yu et Peng - 2010 - Quantification and deconvolution of asymmetric LC-.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\6N8YKJJM\\Yu et Peng - 2010 - Quantification and deconvolution of asymmetric LC-.pdf:application/pdf}
}

@article{schulz-trieglaff_lc-mssim_2008,
	title = {{LC}-{MSsim} – a simulation software for liquid chromatography mass spectrometry data},
	volume = {9},
	issn = {1471-2105},
	url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-423},
	doi = {10.1186/1471-2105-9-423},
	abstract = {Background: Mass Spectrometry coupled to Liquid Chromatography (LC-MS) is commonly used to analyze the protein content of biological samples in large scale studies. The data resulting from an LC-MS experiment is huge, highly complex and noisy. Accordingly, it has sparked new developments in Bioinformatics, especially in the fields of algorithm development, statistics and software engineering. In a quantitative label-free mass spectrometry experiment, crucial steps are the detection of peptide features in the mass spectra and the alignment of samples by correcting for shifts in retention time. At the moment, it is difficult to compare the plethora of algorithms for these tasks. So far, curated benchmark data exists only for peptide identification algorithms but no data that represents a ground truth for the evaluation of feature detection, alignment and filtering algorithms.
Results: We present LC-MSsim, a simulation software for LC-ESI-MS experiments. It simulates ESI spectra on the MS level. It reads a list of proteins from a FASTA file and digests the protein mixture using a user-defined enzyme. The software creates an LC-MS data set using a predictor for the retention time of the peptides and a model for peak shapes and elution profiles of the mass spectral peaks. Our software also offers the possibility to add contaminants, to change the background noise level and includes a model for the detectability of peptides in mass spectra. After the simulation, LC-MSsim writes the simulated data to mzData, a public XML format. The software also stores the positions (monoisotopic m/z and retention time) and ion counts of the simulated ions in separate files.
Conclusion: LC-MSsim generates simulated LC-MS data sets and incorporates models for peak shapes and contaminations. Algorithm developers can match the results of feature detection and alignment algorithms against the simulated ion lists and meaningful error rates can be computed. We anticipate that LC-MSsim will be useful to the wider community to perform benchmark studies and comparisons between computational tools.},
	language = {en},
	number = {1},
	urldate = {2020-11-12},
	journal = {BMC Bioinformatics},
	author = {Schulz-Trieglaff, Ole and Pfeifer, Nico and Gröpl, Clemens and Kohlbacher, Oliver and Reinert, Knut},
	month = dec,
	year = {2008},
	pages = {423},
	file = {Schulz-Trieglaff et al. - 2008 - LC-MSsim – a simulation software for liquid chroma.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\SMXLWBZX\\Schulz-Trieglaff et al. - 2008 - LC-MSsim – a simulation software for liquid chroma.pdf:application/pdf}
}

@article{morris_feature_2005-1,
	title = {Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum},
	volume = {21},
	issn = {1367-4803, 1460-2059},
	url = {https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/bti254},
	doi = {10.1093/bioinformatics/bti254},
	abstract = {Motivation: Mass spectrometry yields complex functional data for which the features of scientiﬁc interest are peaks. A common twostep approach to analyzing these data involves ﬁrst extracting and quantifying the peaks, then analyzing the resulting matrix of peak quantiﬁcations. Feature extraction and quantiﬁcation involves a number of interrelated steps. It is important to perform these steps well, since subsequent analyses condition on these determinations. Also, it is difﬁcult to compare the performance of competing methods for analyzing mass spectrometry data since the true expression levels of the proteins in the population are generally not known.},
	language = {en},
	number = {9},
	urldate = {2020-11-12},
	journal = {Bioinformatics},
	author = {Morris, J. S. and Coombes, K. R. and Koomen, J. and Baggerly, K. A. and Kobayashi, R.},
	month = may,
	year = {2005},
	pages = {1764--1775},
	file = {Morris et al. - 2005 - Feature extraction and quantification for mass spe.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\4N73ZPMZ\\Morris et al. - 2005 - Feature extraction and quantification for mass spe.pdf:application/pdf}
}

@article{zhang_data_2005,
	title = {Data pre-processing in liquid chromatography-mass spectrometry-based proteomics},
	volume = {21},
	issn = {1367-4803, 1460-2059},
	url = {https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/bti660},
	doi = {10.1093/bioinformatics/bti660},
	abstract = {Motivation: In a liquid chromatography–mass spectrometry (LC–MS)based expressional proteomics, multiple samples from different groups are analyzed in parallel. It is necessary to develop a data mining system to perform peak quantification, peak alignment and data quality assurance.},
	language = {en},
	number = {21},
	urldate = {2020-11-12},
	journal = {Bioinformatics},
	author = {Zhang, X. and Asara, J. M. and Adamec, J. and Ouzzani, M. and Elmagarmid, A. K.},
	month = nov,
	year = {2005},
	pages = {4054--4059},
	file = {Zhang et al. - 2005 - Data pre-processing in liquid chromatography-mass .pdf:C\:\\Users\\CR258086\\Zotero\\storage\\SETTYGAK\\Zhang et al. - 2005 - Data pre-processing in liquid chromatography-mass .pdf:application/pdf}
}

@article{wang_dynamic_2010,
	title = {A dynamic wavelet-based algorithm for pre-processing tandem mass spectrometry data},
	volume = {26},
	issn = {1367-4803, 1460-2059},
	url = {https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btq403},
	doi = {10.1093/bioinformatics/btq403},
	abstract = {Motivation: Mass spectrometry (MS)-based proteomics is one of the most commonly used research techniques for identifying and characterizing proteins in biological and medical research. The identiﬁcation of a protein is the critical ﬁrst step in elucidating its biological function. Successful protein identiﬁcation depends on various interrelated factors, including effective analysis of MS data generated in a proteomic experiment. This analysis comprises several stages, often combined in a pipeline or workﬂow. The ﬁrst component of the analysis is known as spectra pre-processing. In this component, the raw data generated by the mass spectrometer is processed to eliminate noise and identify the mass-to-charge ratio (m/z) and intensity for the peaks in the spectrum corresponding to the presence of certain peptides or peptide fragments. Since all downstream analyses depend on the pre-processed data, effective pre-processing is critical to protein identiﬁcation and characterization. There is a critical need for more robust preprocessing algorithms that perform well on tandem mass spectra under a variety of different conditions and can be easily integrated into sophisticated data analysis pipelines for practical wet-lab applications.},
	language = {en},
	number = {18},
	urldate = {2020-11-12},
	journal = {Bioinformatics},
	author = {Wang, P. and Yang, P. and Arthur, J. and Yang, J. Y. H.},
	month = sep,
	year = {2010},
	pages = {2242--2249},
	file = {Wang et al. - 2010 - A dynamic wavelet-based algorithm for pre-processi.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\282TW6Y3\\Wang et al. - 2010 - A dynamic wavelet-based algorithm for pre-processi.pdf:application/pdf}
}

@article{lange_geometric_2007,
	title = {A geometric approach for the alignment of liquid chromatography—mass spectrometry data},
	volume = {23},
	issn = {1460-2059, 1367-4803},
	url = {https://academic.oup.com/bioinformatics/article/23/13/i273/233877},
	doi = {10.1093/bioinformatics/btm209},
	abstract = {Motivation: Liquid chromatography coupled to mass spectrometry (LC-MS) and combined with tandem mass spectrometry (LC-MS/ MS) have become a prominent tool for the analysis of complex proteomic samples. An important step in a typical workflow is the combination of results from multiple LC-MS experiments to improve confidence in the obtained measurements or to compare results from different samples. To do so, a suitable mapping or alignment between the data sets needs to be estimated. The alignment has to correct for variations in mass and elution time which are present in all mass spectrometry experiments.},
	language = {en},
	number = {13},
	urldate = {2020-11-12},
	journal = {Bioinformatics},
	author = {Lange, Eva and Gröpl, Clemens and Schulz-Trieglaff, Ole and Leinenbach, Andreas and Huber, Christian and Reinert, Knut},
	month = jul,
	year = {2007},
	pages = {i273--i281},
	file = {Lange et al. - 2007 - A geometric approach for the alignment of liquid c.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\KNG29BWN\\Lange et al. - 2007 - A geometric approach for the alignment of liquid c.pdf:application/pdf}
}

@article{stancik_simple_2008,
	title = {A simple asymmetric lineshape for fitting infrared absorption spectra},
	volume = {47},
	issn = {09242031},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0924203108000453},
	doi = {10.1016/j.vibspec.2008.02.009},
	abstract = {Almost exclusively, lineshape functions used to model infrared (IR) absorption peaks are based on symmetric frequency distributions. However, in complex systems such as large biological macromolecules in aqueous solutions, the distribution of vibrational frequencies may in fact be asymmetric. In this communication, we show that asymmetry can be introduced to the standard symmetric Lorentzian and Gaussian lineshapes using a simple, easy to implement method. Our technique involves replacing the static width parameter of the symmetric proﬁles with a smoothly varying function that is wave number dependent. In this way, the width varies across the IR band resulting in an asymmetric peak. In our model, the width varies sigmoidally with wave number. As a demonstration, we ﬁt experimental spectra of adenosine 50-monophosphate (AMP).},
	language = {en},
	number = {1},
	urldate = {2020-11-12},
	journal = {Vibrational Spectroscopy},
	author = {Stancik, Aaron L. and Brauns, Eric B.},
	month = may,
	year = {2008},
	pages = {66--69},
	file = {Stancik et Brauns - 2008 - A simple asymmetric lineshape for fitting infrared.pdf:C\:\\Users\\CR258086\\Zotero\\storage\\EIDNBBZY\\Stancik et Brauns - 2008 - A simple asymmetric lineshape for fitting infrared.pdf:application/pdf}
}
