@ARTICLE{Millard2012,
  author = 	 {Millard, P and Letisse, F and Sokol, S and Portais, JC},
  title  = 	 {{IsoCor: correcting MS data in isotope labeling experiments}},
  journal = 	 {Bioinformatics},
  year = 	 {2012},
  month = 	 {May},
  volume = 	 {28},
  number = 	 {9},
  pages = 	 {1294-6},
  abstract = 	 {Mass spectrometry (MS) is widely used for isotopic labeling studies of metabolism and other biological processes. Quantitative applications-e.g. metabolic flux analysis-require tools to correct the raw MS data for the contribution of all naturally abundant isotopes. IsoCor is a software that allows such correction to be applied to any chemical species. Hence it can be used to exploit any isotopic tracer, from well-known ((13)C, (15)N, (18)O, etc) to unusual ((57)Fe, (77)Se, etc) isotopes. It also provides new features-e.g. correction for the isotopic purity of the tracer-to improve the accuracy of quantitative isotopic studies, and implements an efficient algorithm to process large datasets. Its user-friendly interface makes isotope labeling experiments more accessible to a wider biological community.},
  affiliation =  {},
  PMID = 	 {22419781},
  ISSN = 	 {1367-4811},
  pii  = 	 {bts127},
  doi  = 	 {10.1093/bioinformatics/bts127},
  HardcopyLocation = 	 {} 
}

@ARTICLE{Carreer2013,
  author = 	 {Carreer, WJ and Flight, RM and Moseley, HN},
  title  = 	 {{A Computational Framework for High-Throughput Isotopic Natural Abundance Correction of Omics-Level Ultra-High Resolution FT-MS Datasets}},
  journal = 	 {Metabolites},
  year = 	 {2013},
  month = 	 {Sep},
  volume = 	 {3},
  number = 	 {4},
  pages = 	 {},
  abstract = 	 {New metabolomics applications of ultra-high resolution and accuracy mass spectrometry can provide thousands of detectable isotopologues, with the number of potentially detectable isotopologues increasing exponentially with the number of stable isotopes used in newer isotope tracing methods like stable isotope-resolved metabolomics (SIRM) experiments. This huge increase in usable data requires software capable of correcting the large number of isotopologue peaks resulting from SIRM experiments in a timely manner. We describe the design of a new algorithm and software system capable of handling these high volumes of data, while including quality control methods for maintaining data quality. We validate this new algorithm against a previous single isotope correction algorithm in a two-step cross-validation. Next, we demonstrate the algorithm and correct for the effects of natural abundance for both (13)C and (15)N isotopes on a set of raw isotopologue intensities of UDP-N-acetyl-D-glucosamine derived from a (13)C/(15)N-tracing experiment. Finally, we demonstrate the algorithm on a full omics-level dataset. },
  affiliation =  {},
  PMID = 	 {24404440},
  ISSN = 	 {2218-1989},
  doi  = 	 {10.3390/metabo3040853},
  pmc  = 	 {PMC3882318},
  mid  = 	 {NIHMS539461},
  HardcopyLocation = 	 {} 
}

@ARTICLE{Buescher2015,
  author = 	 {Buescher, JM and Antoniewicz, MR and Boros, LG and Burgess, SC and Brunengraber, H and Clish, CB and DeBerardinis, RJ and Feron, O and Frezza, C and Ghesquiere, B and Gottlieb, E and Hiller, K and Jones, RG and Kamphorst, JJ and Kibbey, RG and Kimmelman, AC and Locasale, JW and Lunt, SY and Maddocks, OD and Malloy, C and Metallo, CM and Meuillet, EJ and Munger, J and N�h, K and Rabinowitz, JD and Ralser, M and Sauer, U and Stephanopoulos, G and St-Pierre, J and Tennant, DA and Wittmann, C and Vander Heiden, MG and Vazquez, A and Vousden, K and Young, JD and Zamboni, N and Fendt, SM},
  title  = 	 {{A roadmap for interpreting (13)C metabolite labeling patterns from cells}},
  journal = 	 {Curr Opin Biotechnol},
  year = 	 {2015},
  month = 	 {Aug},
  volume = 	 {34},
  number = 	 {},
  pages = 	 {189-201},
  abstract = 	 {Measuring intracellular metabolism has increasingly led to important insights in biomedical research. (13)C tracer analysis, although less information-rich than quantitative (13)C flux analysis that requires computational data integration, has been established as a time-efficient method to unravel relative pathway activities, qualitative changes in pathway contributions, and nutrient contributions. Here, we review selected key issues in interpreting (13)C metabolite labeling patterns, with the goal of drawing accurate conclusions from steady state and dynamic stable isotopic tracer experiments. },
  affiliation =  {},
  PMID = 	 {25731751},
  ISSN = 	 {1879-0429},
  pii  = 	 {S0958-1669(15)00022-1},
  doi  = 	 {10.1016/j.copbio.2015.02.003},
  pmc  = 	 {PMC4552607},
  mid  = 	 {NIHMS669491},
  HardcopyLocation = 	 {} 
}

@ARTICLE{Jungreuthmayer2016,
  author = 	 {Jungreuthmayer, C and Neubauer, S and Mairinger, T and Zanghellini, J and Hann, S},
  title  = 	 {{ICT: isotope correction toolbox}},
  journal = 	 {Bioinformatics},
  year = 	 {2016},
  month = 	 {Jan},
  volume = 	 {32},
  number = 	 {1},
  pages = 	 {154-6},
  abstract = 	 {Isotope tracer experiments are an invaluable technique to analyze and study the metabolism of biological systems. However, isotope labeling experiments are often affected by naturally abundant isotopes especially in cases where mass spectrometric methods make use of derivatization. The correction of these additive interferences--in particular for complex isotopic systems--is numerically challenging and still an emerging field of research. When positional information is generated via collision-induced dissociation, even more complex calculations for isotopic interference correction are necessary. So far, no freely available tools can handle tandem mass spectrometry data. We present isotope correction toolbox, a program that corrects tandem mass isotopomer data from tandem mass spectrometry experiments. Isotope correction toolbox is written in the multi-platform programming language Perl and, therefore, can be used on all commonly available computer platforms.},
  affiliation =  {},
  PMID = 	 {26382193},
  ISSN = 	 {1367-4811},
  pii  = 	 {btv514},
  doi  = 	 {10.1093/bioinformatics/btv514},
  HardcopyLocation = 	 {} 
}

@ARTICLE{Heinrich2018,
 abstract = {Scientific Reports, doi:10.1038/s41598-018-36293-4},
 author = {Heinrich, P and Kohler, C and Ellmann, L and Kuerner, P and Spang, R and Oefner, PJ and Dettmer, K},
 year = {2018},
 title = {{Correcting for natural isotope abundance and tracer impurity in MS-, MS/MS- and high-resolution-multiple-tracer-data from stable isotope labeling experiments with IsoCorrectoR}},
 urldate = {09.02.2019},
 pages = {17910},
 volume = {8},
 number = {1},
 journal = {Scientific reports},
 doi = {10.1038/s41598-018-36293-4}
}


