Formats:pepXML
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| '''pepXML''' Is a 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''' Is a 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 1.14. | ||
| + | |||
| + | * [http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/schema/pepXML_v114.xsd pepXML 1.14 Schema] (xsd) | ||
| + | |||
| + | == Change History == | ||
| + | |||
| + | * 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== | ==Search-Engine to pepXML converters== | ||
| + | |||
| Sequest: [[Software:Out2XML|Out2XML]] | Sequest: [[Software:Out2XML|Out2XML]] | ||
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| X!Tandem: [[Software:Tandem2XML|Tandem2XML]] | X!Tandem: [[Software:Tandem2XML|Tandem2XML]] | ||
| - | ==PepXML Specification == | ||
| - | The latest version of the format is version 1.14. | + | == Related Formats == |
| - | + | ||
| - | * [http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/schema/pepXML_v114.xsd pepXML 1.14 Schema] (xsd) | + | |
| - | == See Also == | ||
| [http://www.psidev.info/index.php?q=node/40 mzIdentML]: XML standard for MS, MS-MS, MSn or tag searches under development by the HUPO Proteomics Standards Initiative. | [http://www.psidev.info/index.php?q=node/40 mzIdentML]: XML standard for MS, MS-MS, MSn or tag searches under development by the HUPO Proteomics Standards Initiative. | ||
Revision as of 21:22, 28 September 2009
pepXML Is a 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 1.14.
- pepXML 1.14 Schema (xsd)
Change History
- 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.
