The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results

Molecular & Cellular Proteomics - Tập 11 Số 7 - Trang M111.014381-1-M111.014381-10 - 2012
Andrew R. Jones1, Martin Eisenacher2, Gerhard Mayer2, Oliver Kohlbacher3, Jennifer A. Siepen4, Simon J. Hubbard4, J. Selley4, Brian C. Searle5, James H. Shofstahl6, Sean L. Seymour7, Randall K. Julian8, Pierre‐Alain Binz9, Eric W. Deutsch10, Henning Hermjakob11, Florian Reisinger11, Johannes Griss11, Juan Antonio Vizcaíno11, Matthew Chambers12, Angel Pizarro13, David M. Creasy14
1From the ‡Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZJ, UK;
2Medizinisches Proteom-Center, Ruhr-Universitaet Bochum, Universitaetsstr. 150, D-44801 Bochum, Germany
3Center for Bioinformatics, Quantitative Biology Center and Department of Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany
4Faculty of Life Sciences, University of Manchester, M13 9PT, UK
5**Proteome Software Inc., 1340 SW Bertha Blvd. Suite 10, Portland, Oregon, 97219–2039;
6Thermo Fisher Scientific, Inc. 355 River Oaks Parkway, San Jose, CA 95134
7§§AB SCIEX, 110 Marsh Drive, Foster City, California 94404;
8¶¶Indigo BioSystems, Indianapolis, Indiana 46240;
9‖‖Swiss Institute of Bioinformatics, Rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland;
10aInstitute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109;
11bEMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK;
12cDepartment of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee 37212–8575;
13dThe Institute for Translational Medicine and Therapeutics, Biological Research Building II/III, University of Pennsylvania, Philadelphia, Pennsylvania 19104–6160;
14eMatrix Science, 64 Baker Street, London W1U 7GB, UK

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Tài liệu tham khảo

Zhang, 2000, ProFound: An Expert System for Protein Identification Using Mass Spectrometric Peptide Mapping Information, Anal. Chem., 72, 2482, 10.1021/ac991363o

Perkins, 1999, Probability-based protein identification by searching sequence databases using mass spectrometry data, Electrophoresis, 20, 3551, 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2

MacCoss, 2002, Probability-Based Validation of Protein Identifications Using a Modified SEQUEST Algorithm, Anal. Chem., 74, 5593, 10.1021/ac025826t

Geer, 2004, Open Mass Spectrometry Search Algorithm, J. Proteome Res., 3, 958, 10.1021/pr0499491

Fenyö, 2003, A Method for Assessing the Statistical Significance of Mass Spectrometry-Based Protein Identifications Using General Scoring Schemes, Anal. Chem., 75, 768, 10.1021/ac0258709

Colinge, 2003, OLAV: Towards high-throughput tandem mass spectrometry data identification, Proteomics, 3, 1454, 10.1002/pmic.200300485

Ma, 2003, PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry, Rapid Commun. Mass Spectrom., 17, 2337, 10.1002/rcm.1196

Taylor, 2001, Implementation and Uses of Automated de Novo Peptide Sequencing by Tandem Mass Spectrometry, Anal. Chem., 73, 2594, 10.1021/ac001196o

Frank, 2005, PepNovo: De Novo Peptide Sequencing via Probabilistic Network Modeling, Anal. Chem., 77, 964, 10.1021/ac048788h

Mann, 1994, Error-Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence Tags, Anal. Chem., 66, 4390, 10.1021/ac00096a002

Tanner, 2005, InsPecT: Identification of Posttranslationally Modified Peptides from Tandem Mass Spectra, Anal. Chem., 77, 4626, 10.1021/ac050102d

Shilov, 2007, The Paragon Algorithm, a Next Generation Search Engine That Uses Sequence Temperature Values and Feature Probabilities to Identify Peptides from Tandem Mass Spectra, Mol. Cell. Proteomics, 6, 1638, 10.1074/mcp.T600050-MCP200

Lam, 2008, Building consensus spectral libraries for peptide identification in proteomics, Nat. Methods, 5, 873, 10.1038/nmeth.1254

Craig, 2006, Using Annotated Peptide Mass Spectrum Libraries for Protein Identification, J. Proteome Res., 5, 1843, 10.1021/pr0602085

Frewen, 2007, Using BiblioSpec for creating and searching tandem MS peptide libraries, Curr. Protoc. Bioinformatics, 10.1002/0471250953.bi1307s20

Käll, 2008, Assigning significance to peptides identified by tandem mass spectrometry using decoy databases, J. Proteome Res., 7, 29, 10.1021/pr700600n

Carr, 2004, the need for guidelines in publication of peptide and protein identification data: working group on publication guidelines for peptide and protein identification data, Mol. Cell. Proteomics, 3, 531, 10.1074/mcp.T400006-MCP200

Taylor, 2007, The minimum information about a proteomics experiment (MIAPE), Nat. Biotechnol., 25, 887, 10.1038/nbt1329

Desiere, 2006, The PeptideAtlas project, Nucleic Acids Res., 34, D655, 10.1093/nar/gkj040

Jones, 2006, PRIDE: a public repository of protein and peptide identifications for the proteomics community, Nucleic Acids Res., 34, D659, 10.1093/nar/gkj138

Craig, 2004, Open Source System for Analyzing, Validating, and Storing Protein Identification Data, J. Proteome Res., 3, 1234, 10.1021/pr049882h

2009, Credit where credit is overdue, Nat. Biotechnol., 27, 579, 10.1038/nbt0709-579

Martens, 2011, mzML–a community standard for mass spectrometry data, Mol. Cell. Proteomics, 10, 10.1074/mcp.R110.000133

Kerrien, 2007, Broadening the horizon - level 2. 5 of the HUPO-PSI format for molecular interactions, BMC Biol., 5, 44, 10.1186/1741-7007-5-44

Kinsinger, 2012, Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles), Proteomics, 12, 11, 10.1002/pmic.201100562

Kinsinger, 2011, Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles), Mol. Cell. Proteomics, 10, 10.1074/mcp.O111.015446

Kinsinger, 2012, Recommendations for mass spectrometry data quality metrics for open access data (Corollary to the Amsterdam Principles), J. Proteome Res., 11, 1412, 10.1021/pr201071t

Keller, 2005, A uniform proteomics MS/MS analysis platform utilizing open XML file formats, Mol. Syst. Biol., 1, 10.1038/msb4100024

Taylor, 2003, A systematic approach to modeling, capturing, and disseminating proteomics experimental data, Nat. Biotechnol., 21, 247, 10.1038/nbt0303-247

Orchard, 2008, Annual Spring Meeting of the Proteomics Standards Initiative 23–25 April 2008, Toledo, Spain, Proteomics, 8, 4168, 10.1002/pmic.200800555

Orchard, 2006, Proteomics and Beyond A report on the 3rd Annual Spring Workshop of the HUPO-PSI 21–23 April 2006, San Francisco, CA, U. S. A, Proteomics, 6, 4439, 10.1002/pmic.200600452

Orchard, 2006, Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4–6, 2005, Proteomics, 6, 738, 10.1002/pmic.200500868

Orchard, 2007, The HUPO Pre-Congress Proteomics Standards Initiative Workshop HUPO 5th Annual World Congress Long Beach, CA, U. S. A. 28 October-1 November 2006, Proteomics, 7, 1006, 10.1002/pmic.200700014

Vizcaíno, 2007, The PSI formal document process and its implementation on the PSI website, Proteomics, 7, 2355, 10.1002/pmic.200700064

Jones, 2007, The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics, Nat. Biotechnol., 25, 1127, 10.1038/nbt1347

Deutsch, 2008, mzML: A single, unifying data format for mass spectrometer output, Proteomics, 8, 2776, 10.1002/pmic.200890049

Creasy, 2004, Unimod: Protein modifications for mass spectrometry, Proteomics, 4, 1534, 10.1002/pmic.200300744

Montecchi-Palazzi, 2008, The PSI-MOD community standard for representation of protein modification data, Nat. Biotechnol., 26, 864, 10.1038/nbt0808-864

Nesvizhskii, 2003, A Statistical Model for Identifying Proteins by Tandem Mass Spectrometry, Anal. Chem., 75, 4646, 10.1021/ac0341261

Jones, 2009, Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines, Proteomics, 9, 1220, 10.1002/pmic.200800473

Nahnsen, 2011, Probabilistic consensus scoring improves tandem mass spectrometry peptide identification, J. Proteome Res., 10, 3332, 10.1021/pr2002879

Searle, 2008, Improving Sensitivity by Probabilistically Combining Results from Multiple MS/MS Search Methodologies, J. Proteome Res., 7, 245, 10.1021/pr070540w

Stephan, 2006, Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase, Proteomics, 6, 5015, 10.1002/pmic.200600294

Elias, 2007, Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry, Nat. Meth., 4, 207, 10.1038/nmeth1019

Montecchi-Palazzi, 2009, The PSI semantic validator: A framework to check MIAPE compliance of proteomics data, Proteomics, 9, 5112, 10.1002/pmic.200900189

Gloriam, 2010, A Community standard format for the representation of protein affinity reagents, Mol. Cell. Proteomics, 9, 1, 10.1074/mcp.M900185-MCP200

Binz, 2008, Guidelines for reporting the use of mass spectrometry informatics in proteomics, Nat. Biotechnol., 26, 862, 10.1038/nbt0808-862

Gibson, 2008, Guidelines for reporting the use of gel electrophoresis in proteomics, Nat. Biotechnol., 26, 863, 10.1038/nbt0808-863

Orchard, 2007, The minimum information required for reporting a molecular interaction experiment (MIMIx), Nat. Biotechnol., 25, 894, 10.1038/nbt1324

Taylor, 2008, Guidelines for reporting the use of mass spectrometry in proteomics, Nat. Biotechnol., 26, 860, 10.1038/nbt0808-860

Bradshaw, 2006, Reporting protein identification data, Mol. Cell. Proteomics, 5, 787, 10.1074/mcp.E600005-MCP200

Mueller, 2008, An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data, J. Proteome Res., 7, 51, 10.1021/pr700758r

Kessner, 2008, ProteoWizard: open source software for rapid proteomics tools development, Bioinformatics, 24, 2534, 10.1093/bioinformatics/btn323

Sturm, 2008, OpenMS - An open-source software framework for mass spectrometry, BMC Bioinformatics, 9, 163, 10.1186/1471-2105-9-163

Kohlbacher, 2007, TOPP–the OpenMS proteomics pipeline, Bioinformatics, 23, e191, 10.1093/bioinformatics/btl299