Peptide sequence confidence in accurate mass and time analysis and its use in complex proteomics experiments.

Publication Type:

Journal Article


Journal of proteome research, Volume 7, Issue 12, p.5148-56 (2008)


2008, Algorithms, Center-Authored Paper, Chromatography, Liquid, Computational Biology, Hot Temperature, mass spectrometry, Models, Statistical, Peptide Mapping, Peptides, PROTEINS, Proteome, PROTEOMICS, Proteomics Core Facility, Public Health Sciences Division, Reproducibility of Results, Shared Resources, Software


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.