Formats:pepXML
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| Revision as of 18:11, 29 July 2016 Mhoopman (Talk | contribs) (→PepXML Schema) ← Previous diff |
Current revision Luis (Talk | contribs) (→PepXML Schema) |
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| ==PepXML Schema == | ==PepXML Schema == | ||
| - | The latest version of the format is version 1.20. | + | The latest version of the format is version '''1.23'''. |
| - | * [https://sourceforge.net/p/sashimi/code/HEAD/tree/branches/TPP5-Refactor/trans_proteomic_pipeline/schema/pepXML_v120.xsd pepXML 1.20 Schema] (xsd) | + | * [http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v123.xsd pepXML 1.23 Schema] (xsd) |
| - | * [http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v118.xsd pepXML 1.18 Schema] (xsd) | + | * [https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/trans_proteomic_pipeline/schema/ All Versions in revision control] (Subversion) |
| - | * [http://sourceforge.net/p/sashimi/code/HEAD/tree/branches/TPP5-Refactor/trans_proteomic_pipeline/schema/ All Versions in revision control] (Subversion) | + | |
| == Change History == | == 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 | * Revision 1.13 | ||
| **Adds charge states +6 and +7 | **Adds charge states +6 and +7 | ||
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| * Revision 1.10 | * Revision 1.10 | ||
| ** New attributes added | ** New attributes added | ||
| - | |||
| ==Search-Engine to pepXML converters== | ==Search-Engine to pepXML converters== | ||
Current revision
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 |
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.
