High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics

Proteomics
Jacques ColingeLydie Bougueleret

Abstract

In a previous paper we introduced a novel model-based approach (OLAV) to the problem of identifying peptides via tandem mass spectrometry, for which early implementations showed promising performance. We recently further improved this performance to a remarkable level (1-2% false positive rate at 95% true positive rate) and characterized key properties of OLAV like robustness and training set size. We present these results in a synthetic and coherent way along with detailed performance comparisons, a new scoring component making use of peptide amino acidic composition, and new developments like automatic parameter learning. Finally, we discuss the impact of OLAV on the automation of proteomics projects.

Citations

Mar 3, 2007·Journal of the American Society for Mass Spectrometry·Jayson A FalknerPhilip C Andrews
Mar 12, 2011·Journal of Proteome Research·William R CannonDonald A Bryant
Feb 24, 2009·Journal of Proteome Research·Ari M Frank
Sep 23, 2008·Nature Methods·Henry LamRuedi Aebersold
Feb 15, 2011·Biochemistry. Biokhimii︠a︡·N B PolyakovV M Govorun
Aug 21, 2012·Molecular Endocrinology·Lauren B Becnel, Neil J McKenna
Aug 7, 2007·PLoS Computational Biology·Jacques Colinge, Keiryn L Bennett
Jul 18, 2015·Journal of Proteomics·Gerhard MayerMartin Eisenacher
Oct 13, 2006·Proteomics·Frédérique Lisacek
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Jan 18, 2011·Proteomics·Rune MatthiesenAna Sofia Carvalho
Dec 24, 2009·Proteomics·Erik AhrnéFrederique Lisacek
Jan 27, 2010·Proteomics·Eric W DeutschRuedi Aebersold
Jan 14, 2010·Rapid Communications in Mass Spectrometry : RCM·Anton A GoloborodkoMikhail V Gorshkov
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May 23, 2006·Drug Discovery Today·Thodoros Topaloglou
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Jan 2, 2013·Journal of Proteomics·Florent GluckAlexander Scherl
Feb 28, 2008·Molecular & Cellular Proteomics : MCP·Salvador Martínez-BartoloméJesús Vázquez
Mar 8, 2013·International Journal of Molecular Sciences·Monica SoldiTiziana Bonaldi
Apr 23, 2008·Current Protocols in Protein Science·Eugene Kapp, Frédéric Schütz
May 24, 2011·Journal of Proteome Research·Karen Meyer-ArendtNatalie G Ahn
Feb 15, 2005·Journal of Proteome Research·Jacques ColingeLydie Bougueleret
Aug 24, 2007·Analytical Chemistry·Jacques Colinge
Jan 15, 2005·Analytical Chemistry·Jacques ColingeLydie Bougueleret

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