The MzIdentML Data Standard for Mass Spectrometry-based Proteomics Results

Overview

Journal Mol Cell Proteomics

Specialties Biochemistry
Cell Biology
Molecular Biology

Date 2012 Mar 1

PMID 22375074

Citations 92

Authors

Andrew R Jones

Martin Eisenacher

Gerhard Mayer

Oliver Kohlbacher

Jennifer Siepen

Simon J Hubbard

Julian N Selley

Brian C Searle

James Shofstahl

Sean L Seymour

Randall Julian

Pierre-Alain Binz

Eric W Deutsch

Henning Hermjakob

Florian Reisinger

Johannes Griss

Juan Antonio Vizcaino

Matthew Chambers

Angel Pizarro

David Creasy

Affiliations

Soon will be listed here.

Abstract

We report the release of mzIdentML, an exchange standard for peptide and protein identification data, designed by the Proteomics Standards Initiative. The format was developed by the Proteomics Standards Initiative in collaboration with instrument and software vendors, and the developers of the major open-source projects in proteomics. Software implementations have been developed to enable conversion from most popular proprietary and open-source formats, and mzIdentML will soon be supported by the major public repositories. These developments enable proteomics scientists to start working with the standard for exchanging and publishing data sets in support of publications and they provide a stable platform for bioinformatics groups and commercial software vendors to work with a single file format for identification data.

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References

Shilov I, Seymour S, Patel A, Loboda A, Tang W, Keating S . 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. 2007; 6(9):1638-55. DOI: 10.1074/mcp.T600050-MCP200. View

Frank A, Pevzner P . PepNovo: de novo peptide sequencing via probabilistic network modeling. Anal Chem. 2005; 77(4):964-73. DOI: 10.1021/ac048788h. View

Sturm M, Bertsch A, Gropl C, Hildebrandt A, Hussong R, Lange E . OpenMS - an open-source software framework for mass spectrometry. BMC Bioinformatics. 2008; 9:163. PMC: 2311306. DOI: 10.1186/1471-2105-9-163. View

Binz P, Barkovich R, Beavis R, Creasy D, Horn D, Julian Jr R . Guidelines for reporting the use of mass spectrometry informatics in proteomics. Nat Biotechnol. 2008; 26(8):862. DOI: 10.1038/nbt0808-862. View

Montecchi-Palazzi L, Beavis R, Binz P, Chalkley R, Cottrell J, Creasy D . The PSI-MOD community standard for representation of protein modification data. Nat Biotechnol. 2008; 26(8):864-6. DOI: 10.1038/nbt0808-864. View

Taylor C, Paton N, Lilley K, Binz P, Julian Jr R, Jones A . The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol. 2007; 25(8):887-93. DOI: 10.1038/nbt1329. View

Creasy D, Cottrell J . Unimod: Protein modifications for mass spectrometry. Proteomics. 2004; 4(6):1534-6. DOI: 10.1002/pmic.200300744. View

Craig R, Cortens J, Fenyo D, Beavis R . Using annotated peptide mass spectrum libraries for protein identification. J Proteome Res. 2006; 5(8):1843-9. DOI: 10.1021/pr0602085. View

Craig R, Cortens J, Beavis R . Open source system for analyzing, validating, and storing protein identification data. J Proteome Res. 2004; 3(6):1234-42. DOI: 10.1021/pr049882h. View

10.

Montecchi-Palazzi L, Kerrien S, Reisinger F, Aranda B, Jones A, Martens L . The PSI semantic validator: a framework to check MIAPE compliance of proteomics data. Proteomics. 2009; 9(22):5112-9. DOI: 10.1002/pmic.200900189. View

11.

Orchard S, Albar J, Deutsch E, Binz P, Jones A, Creasy D . Annual spring meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain. Proteomics. 2008; 8(20):4168-72. DOI: 10.1002/pmic.200800555. View

12.

Colinge J, Masselot A, Giron M, Dessingy T, Magnin J . OLAV: towards high-throughput tandem mass spectrometry data identification. Proteomics. 2003; 3(8):1454-63. DOI: 10.1002/pmic.200300485. View

13.

Gibson F, Anderson L, Babnigg G, Baker M, Berth M, Binz P . Guidelines for reporting the use of gel electrophoresis in proteomics. Nat Biotechnol. 2008; 26(8):863-4. DOI: 10.1038/nbt0808-863. View

14.

. Credit where credit is overdue. Nat Biotechnol. 2009; 27(7):579. DOI: 10.1038/nbt0709-579. View

15.

Elias J, Gygi S . Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods. 2007; 4(3):207-14. DOI: 10.1038/nmeth1019. View

16.

Gloriam D, Orchard S, Bertinetti D, Bjorling E, Bongcam-Rudloff E, Borrebaeck C . A community standard format for the representation of protein affinity reagents. Mol Cell Proteomics. 2009; 9(1):1-10. PMC: 2808255. DOI: 10.1074/mcp.M900185-MCP200. View

17.

Keller A, Eng J, Zhang N, Li X, Aebersold R . A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol Syst Biol. 2006; 1:2005.0017. PMC: 1681455. DOI: 10.1038/msb4100024. View

18.

Fenyo D, Beavis R . A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal Chem. 2003; 75(4):768-74. DOI: 10.1021/ac0258709. View

19.

Taylor C, Paton N, Garwood K, Kirby P, Stead D, Yin Z . A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat Biotechnol. 2003; 21(3):247-54. DOI: 10.1038/nbt0303-247. View

20.

Carr S, Aebersold R, Baldwin M, Burlingame A, Clauser K, Nesvizhskii A . 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. 2004; 3(6):531-3. DOI: 10.1074/mcp.T400006-MCP200. View