Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics

PeptideAtlas, SRMAtlas, and PASSEL are Web‐accessible resources to support discovery and targeted proteomics research. PeptideAtlas is a multi‐species compendium of shotgun proteomic data provided by the scientific community; SRMAtlas is a resource of high‐quality, complete proteome SRM assays generated in a consistent manner for the targeted identification and quantification of proteins; and PASSEL is a repository that compiles and represents selected reaction monitoring data, all in an easy‐to‐use interface. The databases are generated from native mass spectrometry data files that are analyzed in a standardized manner including statistical validation of the results. Each resource offers search functionalities and can be queried by user‐defined constraints; the query results are provided in tables or are graphically displayed. PeptideAtlas, SRMAtlas, and PASSEL are publicly available freely via the Web site http://www.peptideatlas.org. In this protocol, we describe the use of these resources, we highlight how to submit, search, collate and download data. Curr. Protoc. Bioinform. 46:13.25.1‐13.25.28. © 2014 by John Wiley & Sons, Inc.

[1]  Andrew R. Jones,et al.  ProteomeXchange provides globally co-ordinated proteomics data submission and dissemination , 2014, Nature Biotechnology.

[2]  Nichole L. King,et al.  The PeptideAtlas Project , 2010, Proteome Bioinformatics.

[3]  Nichole L. King,et al.  Development and validation of a spectral library searching method for peptide identification from MS/MS , 2007, Proteomics.

[4]  Lennart Martens,et al.  PRIDE: The proteomics identifications database , 2005, Proteomics.

[5]  Eric W Deutsch,et al.  State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project. , 2014, Journal of proteome research.

[6]  Christopher S. Oehmen,et al.  A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics , 2008, Bioinform..

[7]  Chris F. Taylor,et al.  A common open representation of mass spectrometry data and its application to proteomics research , 2004, Nature Biotechnology.

[8]  Ruedi Aebersold,et al.  The Mtb proteome library: a resource of assays to quantify the complete proteome of Mycobacterium tuberculosis. , 2013, Cell host & microbe.

[9]  James P. Reilly,et al.  A computational approach toward label-free protein quantification using predicted peptide detectability , 2006, ISMB.

[10]  Brendan MacLean,et al.  Skyline: an open source document editor for creating and analyzing targeted proteomics experiments , 2010, Bioinform..

[11]  Amos Bairoch,et al.  neXtProt: a knowledge platform for human proteins , 2011, Nucleic Acids Res..

[12]  Eric W. Deutsch,et al.  A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis , 2013, Nature.

[13]  Henry H. N. Lam,et al.  PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows , 2008, EMBO reports.

[14]  Robertson Craig,et al.  Open source system for analyzing, validating, and storing protein identification data. , 2004, Journal of proteome research.

[15]  Juan Antonio Vizcaíno,et al.  From Peptidome to PRIDE: Public proteomics data migration at a large scale , 2013, Proteomics.

[16]  John Chilton,et al.  Using iRT, a normalized retention time for more targeted measurement of peptides , 2012, Proteomics.

[17]  Nichole L. King,et al.  Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry , 2004, Genome Biology.

[18]  R. Aebersold,et al.  Scoring proteomes with proteotypic peptide probes , 2005, Nature Reviews Molecular Cell Biology.

[19]  Eric W. Deutsch,et al.  The PeptideAtlas project , 2005, Nucleic Acids Res..

[20]  Ruedi Aebersold,et al.  N-Glycoprotein SRMAtlas , 2013, Molecular & Cellular Proteomics.

[21]  R. Aebersold,et al.  mProphet: automated data processing and statistical validation for large-scale SRM experiments , 2011, Nature Methods.

[22]  Natalie I. Tasman,et al.  A guided tour of the Trans‐Proteomic Pipeline , 2010, Proteomics.

[23]  Ruedi Aebersold,et al.  Using the Human Plasma PeptideAtlas to study human plasma proteins. , 2011, Methods in molecular biology.

[24]  J. Mesirov,et al.  Prediction of high-responding peptides for targeted protein assays by mass spectrometry , 2009, Nature Biotechnology.

[25]  Lennart Martens,et al.  TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists* , 2011, Molecular & Cellular Proteomics.

[26]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[27]  W. Ens,et al.  Sequence-specific retention calculator. A family of peptide retention time prediction algorithms in reversed-phase HPLC: applicability to various chromatographic conditions and columns. , 2007, Analytical chemistry.

[28]  Ludovic C. Gillet,et al.  Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis* , 2012, Molecular & Cellular Proteomics.

[29]  Lennart Martens,et al.  mzML—a Community Standard for Mass Spectrometry Data* , 2010, Molecular & Cellular Proteomics.

[30]  R. Aebersold,et al.  A uniform proteomics MS/MS analysis platform utilizing open XML file formats , 2005, Molecular systems biology.

[31]  Luis Mendoza,et al.  PASSEL: The PeptideAtlas SRMexperiment library , 2012, Proteomics.

[32]  Daniel B. Martin,et al.  Computational prediction of proteotypic peptides for quantitative proteomics , 2007, Nature Biotechnology.