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.
Highlights
From the ‡Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZJ, UK; §Medizinisches Proteom-Center, Ruhr-Universitaet Bochum, Universitaetsstr. 150, D-44801 Bochum, Germany; ¶Center for Bioinformatics, Quantitative Biology Center, and Department of Computer Science, University of Tubingen, Sand 14, 72076 Tubingen, Germany; ʈFaculty of Life Sciences, University of Manchester, M13 9PT, UK; **Proteome Software Inc., 1340 SW Bertha Blvd
The mzIdentML format stores peptide and protein identifications based on mass spectrometry (Fig. 1) and captures metadata about methods, parameters, and quality metrics
The mzIdentML standard has been developed over several years within the Proteomics Standards Initiative (PSI)’s standardization process, which is open to all interested parties and transparent at each stage
Summary
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. The mzIdentML standard is, similar to mzML, coping with this requirement and is able to support meta data associated with the identification of peptides and proteins
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