Title: State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet.

Authors: Deutsch, Eric W; Sun, Zhi; Campbell, David; Kusebauch, Ulrike; Chu, Caroline S; Mendoza, Luis; Shteynberg, David; Omenn, Gilbert S; Moritz, Robert L

Published In J Proteome Res, (2015 Sep 04)

Abstract: The Human PeptideAtlas is a compendium of the highest quality peptide identifications from over 1000 shotgun mass spectrometry proteomics experiments collected from many different laboratories, all reanalyzed through a uniform processing pipeline. The latest 2015-03 build contains substantially more input data than past releases, is mapped to a recent version of our merged reference proteome, and uses improved informatics processing and the development of the AtlasProphet to provide the highest quality results. Within the set of ∼20,000 neXtProt primary entries, 14,070 (70%) are confidently detected in the latest build, 5% are ambiguous, 9% are redundant, leaving the total percentage of proteins for which there are no mapping detections at just 16% (3166), all derived from over 133 million peptide-spectrum matches identifying more than 1 million distinct peptides using AtlasProphet to characterize and classify the protein matches. Improved handling for detection and presentation of single amino-acid variants (SAAVs) reveals the detection of 5326 uniquely mapping SAAVs across 2794 proteins. With such a large amount of data, the control of false positives is a challenge. We present the methodology and results for maintaining rigorous quality along with a discussion of the implications of the remaining sources of errors in the build.

PubMed ID: 26139527

MeSH Terms: Amino Acid Sequence; Amino Acid Substitution; Databases, Protein*; Humans; Molecular Sequence Data; Proteins/chemistry*; Proteomics*; Sequence Homology, Amino Acid