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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.


PepXML Schema

The latest version of the format is version 1.23.

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.

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