@article{Michalski2011,
author = {Michalski, Annette and Cox, Juergen and Mann, Matthias},
doi = {10.1021/pr101060v},
issn = {15353893},
journal = {Journal of Proteome Research},
keywords = {dynamic range,peptide identification,proteome identification,shotgun proteomics,tandem mass spectrometry},
number = {4},
pages = {1785--1793},
pmid = {21309581},
title = {{More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS}},
volume = {10},
year = {2011}
}
@article{Lawson2017,
author = {Lawson, Thomas Nigel and Weber, Ralf J. M. and Jones, Martin R. and Chetwynd, Andrew J. and {Rodriguez Blanco}, Giovanny Alejandro and {Di Guida}, Riccardo and Viant, Mark R. and Dunn, Warwick B},
doi = {10.1021/acs.analchem.6b04358},
issn = {0003-2700},
journal = {Analytical Chemistry},
pages = {acs.analchem.6b04358},
title = {{msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics}},
url = {http://pubs.acs.org/doi/abs/10.1021/acs.analchem.6b04358},
year = {2017}
}
@article{Zhou2014,
author = {Zhou, Jiarui and Weber, Ralf J M and Allwood, J William and Mistrik, Robert and Zhu, Zexuan and Ji, Zhen and Chen, Siping and Dunn, Warwick B and He, Shan and Viant, Mark R},
doi = {10.1093/bioinformatics/btt711},
issn = {1367-4811},
journal = {Bioinformatics (Oxford, England)},
number = {4},
pages = {581--3},
pmid = {24336413},
title = {{HAMMER: automated operation of mass frontier to construct in silico mass spectral fragmentation libraries.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3928522\&tool=pmcentrez\&rendertype=abstract},
volume = {30},
year = {2014}
}
@article{Ye2010,
author = {Ye, Ding and Fu, Yan and Sun, Rui Xiang and Wang, Hai Peng and Yuan, Zuo Fei and Chi, Hao and He, Si Min},
doi = {10.1093/bioinformatics/btq185},
isbn = {1367-4803},
issn = {13674803},
journal = {Bioinformatics},
pages = {399--406},
pmid = {20529934},
title = {{Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate}},
volume = {26},
year = {2010}
}

@article{Neumann2013,
author = {Neumann, Steffen and Thum, Andrea and B\"{o}ttcher, Christoph},
doi = {10.1007/s11306-012-0401-0},
isbn = {1573-3882},
issn = {1573-3882},
journal = {Metabolomics},
pages = {84--91},
title = {{Nearline acquisition and processing of liquid chromatography-tandem mass spectrometry data}},
year = {2013}
}

@article{Horai2008,
abstract = {Metabolomics is one of the most important topics in biology and medical science. In metabolomics, metabolites from biological samples are measured by mass spectrometry (MS) and then identified by database searches for similar spectra. Since spectra from the same compound may differ depending on measurement conditions, comparison measure is a crucial issue for identifying compounds from their spectra. A standard method for comparison is normalized dot product or cosine correlation between spectral peaks. We discuss the weighting scheme for preprocessing peak intensities and demonstrate comparison results for about 9,000 spectra in our publicly available MassBank database (http://www. massbank.jp/).},
author = {Horai, Hisayuki and Arita, Masanori and Nishioka, Takaaki},
doi = {10.1109/BMEI.2008.339},
isbn = {9780769531182},
issn = {0769531180},
journal = {BioMedical Engineering and Informatics: New Development and the Future - Proceedings of the 1st International Conference on BioMedical Engineering and Informatics, BMEI 2008},
pages = {853--857},
title = {{Comparison of ESI-MS spectra in MassBank database}},
volume = {2},
year = {2008}
}

@article{stein1994optimization,
author = {Stein, Stephen E and Scott, Donald R},
journal = {Journal of the American Society for Mass Spectrometry},
number = {9},
pages = {859--866},
publisher = {Elsevier},
title = {{Optimization and testing of mass spectral library search algorithms for compound identification}},
volume = {5},
year = {1994}
}


