Getting more out of mass spectrophotometry-based proteomics using supervised learning approaches and on-the-fly data analysis

Dumontier M. (2010) Mass Spectrometry: Protein Identification Strategies. OISB : The ABC of Mass Spectrophotometry for biology Workshop.

 

Eng, J. K., B. Fischer, J. Grossmann and M. J. Maccoss (2008). "A fast SEQUEST cross correlation algorithm." J Proteome Res 7(10): 4598-4602.

 

Eng, J. K., A. L. McCormack and J. R. Yates (1994). "An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein base de données." J Am Soc Mass Spectrom 5(11): 976-989.

 

Frank, A. M., Savitski, M. M., Nielsen, M. L., Zubarev, R. A., & Pevzner, P. A. (2007). De novo peptide sequencing and identification with precision mass spectrometry. Journal of proteome research 6(1), 114–123. doi:10.1021/pr060271u

 

Kall, L., J. D. Canterbury, J. Weston, W. S. Noble and M. J. MacCoss (2007). "Semi-supervised learning for peptide identification from shotgun proteomics datasets." Nat Methods 4(11): 923-925.

 

Klammer, A. A., C. Y. Park and W. S. Noble (2009). "Statistical calibration of the SEQUEST XCorr function." J Proteome Res 8(4): 2106-2113.

 

Ma K., Vitek O. Nesvizhkii A.I. (2012). A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet. BMC Bioinformatics 13(Suppl 16):S1 http://www.biomedcentral.com/1471-2105/13/S16/S1.

 

McHugh, L., & Arthur, J. W. (2008). Computational methods for protein identification from mass spectrometry data. PLoS computational biology 4(2), e12. doi:10.1371/journal.pcbi.0040012.

 

Swan, A. L., Mobasheri, A., Allaway, D., Liddell, S., & Bacardit, J. (2013). Application of machine learning to proteomics data: classification and biomarker identification in postgenomics biology. Omics : a journal of integrative biology 17(12), 595–610. doi:10.1089/omi.2013.0017

 

Tabb, D. L. (2015). "The SEQUEST family tree." J Am Soc Mass Spectrom 26(11): 1814-1819.

 

Tabb, D. L., W. H. McDonald and J. R. Yates, 3rd (2002). "DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics." J Proteome Res 1(1): 21-26.

 

Vitek O (2009.) Getting Started in Computational Mass Spectrometry–Based Proteomics. PLoS Comput Biol 5(5): e1000366. https://doi.org/10.1371/journal.pcbi.1000366

 

Willemin, M.-E. (2014). Toxicokinetic modeling of cis and trans isomers of permethrin and their metabolytes in rat and of their metabolism in human hepatocytes. Thesis. Université de Technologie de Compiègne

 

Xu, T., S. K. Park, J. D. Venable, J. A. Wohlschlegel, J. K. Diedrich, D. Cociorva, B. Lu, L. Liao, J. Hewel, X. Han, C. C. L. Wong, B. Fonslow, C. Delahunty, Y. Gao, H. Shah and J. R. Yates, 3rd (2015). "ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity." J Proteomics 129: 16-24.

 

Yates, J. R., 3rd (2015). "Pivotal role of computers and software in mass spectrometry - SEQUEST and 20 years of tandem MS base de données searching." J Am Soc Mass Spectrom 26(11): 1804-1813.

 

Zhang, J., J. Li, H. Xie, Y. Zhu and F. He (2007). "A new strategy to filter out false positive identifications of peptides in SEQUEST base de données search results." Proteomics 7(22): 4036-4044.