Formats:pepXML
From SPCTools
pepXML Is an open data format developed at the SPC/Institute for Systems biology for the storage, exchange, and processing of peptide sequence assignments of MS/MS scans. pepXML is intended to provide a common data output format for many different MS/MS search engines and subsequent peptide-level analyses. Several search engines already have native support for outputting pepXML and converters are available to transform output files to pepXML.
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PepXML Schema
The latest version of the format is version 1.23.
- pepXML 1.23 Schema (xsd)
- All Versions in revision control (Subversion)
Change History
- Revision 1.22 (and changes from 1.21)
- Adds decoy analysis tags
- Expands list of possible aa- and term- modification symbols
- Adds new terminal mod elements for PTMProphet results
- Adds support for PEFF-derived aa substitutions (new aminoacid_substitution tag, new attributes to mod_aminoacid_mass tag)
- Changes type of massdiff attribute from string to more correct float, as well as calc_pI to double
- Adds Calibr and Novor to engineType list
- Revision 1.20
- Adds cross-linked PSM representation
- Revision 1.13
- Adds charge states +6 and +7
- Revision 1.12
- Adds non-parametric model_dis_type
- Adds "X! Tandem (k-score)" search engine
- Allows mixed unbounded sequence of mixturemodel_distributionand new mixturemodel elements
- Adds search_engine attribute to msms_run_summary
- Changes unused out_data, out_data_type attributes from required to optional
- Revision 1.11
- Schema updated to include omssa and myrimatch search engine names
- Revision 1.10
- New attributes added
Search-Engine to pepXML converters
Sequest: Out2XML
Mascot: Mascot2XML
X!Tandem: Tandem2XML
Related Formats
mzIdentML: XML standard for MS, MS-MS, MSn or tag searches under development by the HUPO Proteomics Standards Initiative.
Change Policy
Requests for changes to the pepXML schema should be submitted to the spctools-dev mailing list.
