Peptide sequence confidence in accurate mass and time analysis and its use in complex proteomics experiments.
We present new algorithms and a software implementation for assigning confidence to peptide sequence assignments obtained through classic accurate mass and retention time (AMT) matching techniques, as well as methods for integrating these assignments with standard proteomics workflows. The algorithms are intended to increase the number of peptides and proteins identified (and, when applicable, quantitated by isotopic labeling) among related proteomics experiments that use high-resolution mass spectrometry instrumentation. The motivations for our extensions include the need to exploit high-resolution data to support highly complex proteomics experiments, especially those involving extensive off-line fractionation, to which recent label-free workflows might not easily generalize.
May
Damon
D
Molecular Diagnostics Program, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
Liu
Yan
Y
Law
Wendy
W
Fitzgibbon
Matt
M
Wang
Hong
H
Hanash
Samir
S
McIntosh
Martin
M
D000465:Algorithms; D002853:Chromatography, Liquid / Q000379:methods; D019295:Computational Biology / Q000379:methods*; D006358:Hot Temperature; D013058:Mass Spectrometry / Q000379:methods; D015233:Models, Statistical; D010449:Peptide Mapping / Q000379:methods*; D010455:Peptides / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry; D020543:Proteome / Q000032:analysis / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software
D010455:Peptides; D011506:Proteins; D020543:Proteome