State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet.
Eric W. Deutsch,Zhi Sun,David S. Campbell,Ulrike Kusebauch,Caroline S. Chu,Luis Mendoza,David Shteynberg,Gilbert S. Omenn,Gilbert S. Omenn,Robert L. Moritz +9 more
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TLDR
Improved handling for detection and presentation of single amino-acid variants (SAAVs) reveals the detection of 5326 uniquely mapping SAAVs across 2794 proteins.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.read more
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Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome
Ulrike Kusebauch,David S. Campbell,Eric W. Deutsch,Caroline S. Chu,Douglas A. Spicer,Mi-Youn Brusniak,Joseph Slagel,Zhi Sun,Jeffrey Stevens,Barbara Grimes,David Shteynberg,Michael R. Hoopmann,Peter Blattmann,Alexander V. Ratushny,Oliver Rinner,Paola Picotti,Christine Carapito,Chung-Ying Huang,Meghan Kapousouz,Henry H N Lam,Tommy Tran,Emek Demir,John D. Aitchison,John D. Aitchison,Chris Sander,Leroy Hood,Ruedi Aebersold,Ruedi Aebersold,Robert L. Moritz +28 more
TL;DR: The generation and verification of a compendium of highly specific assays that enable quantification of 99.7% of the 20,277 annotated human proteins by the widely accessible, sensitive, and robust targeted mass spectrometric method selected reaction monitoring, SRM are described.
Journal ArticleDOI
Alternative Splicing May Not Be the Key to Proteome Complexity
TL;DR: Most alternative exons do not seem to be under selective pressure, suggesting that a large majority of predicted alternative transcripts may not even be translated into proteins.
Journal ArticleDOI
Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry–Based Assays
Andrew N. Hoofnagle,Jeffrey R. Whiteaker,Steven A. Carr,Eric Kuhn,Tao Liu,Sam A. Massoni,Stefani N. Thomas,Raymond R. Townsend,Lisa J. Zimmerman,Emily S. Boja,Jing Chen,Daniel L. Crimmins,Sherri R. Davies,Yuqian Gao,Tara Hiltke,Karen A. Ketchum,Christopher R. Kinsinger,Mehdi Mesri,Matthew R. Meyer,Wei-Jun Qian,Regine M. Schoenherr,Mitchell G. Scott,Tujin Shi,Gordon Whiteley,John A. Wrobel,Chaochao Wu,Brad Ackermann,Ruedi Aebersold,David R. Barnidge,David M. Bunk,Nigel J. Clarke,Jordan B. Fishman,Russ P. Grant,Ulrike Kusebauch,Mark M. Kushnir,Mark S. Lowenthal,Robert L. Moritz,Hendrik Neubert,Scott D. Patterson,Alan L. Rockwood,John C. Rogers,Ravinder J. Singh,Jennifer E. Van Eyk,Steven H. Wong,Shucha Zhang,Daniel W. Chan,Xian Chen,Matthew J. Ellis,Daniel C. Liebler,Karin D. Rodland,Henry Rodriguez,Richard D. Smith,Zhen Zhang,Hui Zhang,Amanda G. Paulovich +54 more
TL;DR: The Clinical Proteomic Tumor Analysis Consortium of the National Cancer Institute has collaborated with clinical laboratorians, peptide manufacturers, metrologists, representatives of the pharmaceutical industry, and other professionals to develop a consensus set of recommendations for peptide procurement, characterization, storage, and handling.
Journal ArticleDOI
The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays
Jochen M. Schwenk,Gilbert S. Omenn,Zhi Sun,David S. Campbell,Mark S. Baker,Christopher M. Overall,Ruedi Aebersold,Robert L. Moritz,Eric W. Deutsch +8 more
TL;DR: The history of the HPPP and the advances of human plasma proteomics in general are reviewed, including several recent achievements, and the latest 2017-04 build of Human Plasma PeptideAtlas is presented, which yields ∼43 million peptide-spectrum matches and 122,730 distinct peptide sequences from 178 individual experiments.
Journal ArticleDOI
An update on sORFs.org: a repository of small ORFs identified by ribosome profiling.
TL;DR: This update elaborates on the major improvements implemented since the initial release of sORFs.org, and a full PRIDE-ReSpin pipeline was now released, reprocessing publicly available MS-based proteomics PRIDE datasets, reporting on true translation events.
References
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