The mzIdentML data standard for mass spectrometry-based proteomics results

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 Vizcaíno; Matthew Chambers; Angel Pizarro; David Creasy

doi:10.1074/mcp.M111.014381

The mzIdentML data standard for mass spectrometry-based proteomics results

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 Vizcaíno, Matthew Chambers, Angel Pizarro, David Creasy

Research output: Contribution to journal › Article › peer-review

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. © 2012 by The American Society for Biochemistry and Molecular Biology, Inc.

Original language	English
Journal	Molecular and Cellular Proteomics
Volume	11
Issue number	7
DOIs	https://doi.org/10.1074/mcp.M111.014381
Publication status	Published - Jul 2012

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Jones, A. R., Eisenacher, M., Mayer, G., Kohlbacher, O., Siepen, J., Hubbard, S. J., Selley, J. N., Searle, B. C., Shofstahl, J., Seymour, S. L., Julian, R., Binz, P. A., Deutsch, E. W., Hermjakob, H., Reisinger, F., Griss, J., Vizcaíno, J. A., Chambers, M., Pizarro, A., & Creasy, D. (2012). The mzIdentML data standard for mass spectrometry-based proteomics results. Molecular and Cellular Proteomics, 11(7). https://doi.org/10.1074/mcp.M111.014381

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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. {\textcopyright} 2012 by The American Society for Biochemistry and Molecular Biology, Inc.",

author = "Jones, {Andrew R.} and Martin Eisenacher and Gerhard Mayer and Oliver Kohlbacher and Jennifer Siepen and Hubbard, {Simon J.} and Selley, {Julian N.} and Searle, {Brian C.} and James Shofstahl and Seymour, {Sean L.} and Randall Julian and Binz, {Pierre Alain} and Deutsch, {Eric W.} and Henning Hermjakob and Florian Reisinger and Johannes Griss and Vizca{\'i}no, {Juan Antonio} and Matthew Chambers and Angel Pizarro and David Creasy",

note = "BB/F004605/1, Biotechnology and Biological Sciences Research Council, United KingdomBB/G010781/1, Biotechnology and Biological Sciences Research Council, United KingdomBB/H024654/1, Biotechnology and Biological Sciences Research Council, United KingdomBB/I00095X/1, Biotechnology and Biological Sciences Research Council, United KingdomN01-HV-28179, NHLBI NIH HHS, United StatesP50 GM076547, NIGMS NIH HHS, United StatesR01 GM087221, NIGMS NIH HHS, United StatesWT085949MA, Wellcome Trust, United Kingdom",

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doi = "10.1074/mcp.M111.014381",

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Jones, AR, Eisenacher, M, Mayer, G, Kohlbacher, O, Siepen, J, Hubbard, SJ, Selley, JN, Searle, BC, Shofstahl, J, Seymour, SL, Julian, R, Binz, PA, Deutsch, EW, Hermjakob, H, Reisinger, F, Griss, J, Vizcaíno, JA, Chambers, M, Pizarro, A & Creasy, D 2012, 'The mzIdentML data standard for mass spectrometry-based proteomics results', Molecular and Cellular Proteomics, vol. 11, no. 7. https://doi.org/10.1074/mcp.M111.014381

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AU - Jones, Andrew R.

AU - Eisenacher, Martin

AU - Mayer, Gerhard

AU - Kohlbacher, Oliver

AU - Siepen, Jennifer

AU - Hubbard, Simon J.

AU - Selley, Julian N.

AU - Searle, Brian C.

AU - Shofstahl, James

AU - Seymour, Sean L.

AU - Julian, Randall

AU - Binz, Pierre Alain

AU - Deutsch, Eric W.

AU - Hermjakob, Henning

AU - Reisinger, Florian

AU - Griss, Johannes

AU - Vizcaíno, Juan Antonio

AU - Chambers, Matthew

AU - Pizarro, Angel

AU - Creasy, David

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PY - 2012/7

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AB - 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. © 2012 by The American Society for Biochemistry and Molecular Biology, Inc.

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DO - 10.1074/mcp.M111.014381

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SN - 1535-9476

VL - 11

JO - Molecular and Cellular Proteomics

JF - Molecular and Cellular Proteomics

IS - 7

ER -

The mzIdentML data standard for mass spectrometry-based proteomics results

Abstract

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