title: State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet.
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.
authors.affiliation: Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States.
authors.forename: Eric W
authors.initials: EW
authors.lastname: Deutsch
authors.affiliation: Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States.
authors.forename: Zhi
authors.initials: Z
authors.lastname: Sun
authors.affiliation: Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States.
authors.forename: David
authors.initials: D
authors.lastname: Campbell
authors.affiliation: Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Kusebauch
authors.affiliation: Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States.
authors.forename: Caroline S
authors.initials: CS
authors.lastname: Chu
authors.affiliation: Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States.
authors.forename: Luis
authors.initials: L
authors.lastname: Mendoza
authors.affiliation: Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States.
authors.forename: David
authors.initials: D
authors.lastname: Shteynberg
authors.affiliation: Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States.|Departments of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics and School of Public Health, University of Michigan , Ann Arbor, Michigan 48109, United States.
authors.forename: Gilbert S
authors.initials: GS
authors.lastname: Omenn
authors.affiliation: Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Moritz
mesh_terms: D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D030562:Databases, Protein; D006801:Humans; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics; D017386:Sequence Homology, Amino Acid
chemical_list: D011506:Proteins
keywords: Human Proteome Project; PeptideAtlas; observed proteome; repositories; shotgun proteomics; tandem mass spectrometry