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.

Contents 1 PepXML Schema 2 Change History 3 Search-Engine to pepXML converters 4 Related Formats 5 Change Policy

PepXML Schema

The latest version of the format is version 1.20.

• pepXML 1.20 Schema (xsd)
• All Versions in revision control (Subversion)

Change History

• 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.