The HUPO PSI Mass Spectrometry Standards Working Group (MSS WG) has developed a specification for a standardized format for the exchange and transmission of transition lists for selected reaction monitoring (SRM) experiments. This specification has now completed rigorous review with the PSI document process and is complete. Please email the list email@example.com with your questions, comments, and suggestions.
TraML Development Timeline
- 2010-03-31 TraML 0.9.4 draft posted
- 2010-07-01 TraML 0.9.4 submitted as 1.0.0RC1 to PSI document process
- 2011-08-23 TraML 0.9.5 draft posted
- 2011-12-12 TraML 1.0.0 released
New TraML 1.0.0 Finished Specification
The information and documents in this subsection are related to TraML 1.0.0, now complete in its development cycle. There are currently no open issues for a follow-on version. Everyone is encouraged to examine and implement the formatas widely as possible.
XML schema definition files (.xsd):
- TraML1.0.0.xsd (main schema)
- Full Specification Document: TraML188.8.131.52_specificationDocument.pdf
- HTML schema documentation for TraML1.0.0
- Please cite this journal article when referencing TraML: Deutsch et al. 2011, MCP, 10, R111.015040
Controlled Vocabulary and Mapping Files:
- Latest semantic validator mapping file, which defines where certain controlled vocabulary terms may be used in a document.
- Latest development version of the CV in OBO 1.2 format
You can explore the CV at the NCBO BioPortal, or at the EBI OLS (Ontology Lookup Service), or with the Java desktop application OBO-Edit.
Sample instance documents for all relevant formats:
- Yeast_ATAQS_gen.TraML (6 MB)
- On-line TraML converter using Compomics jTraML (current at version 1.0.0)
- On-line TraML validator at OpenMS (current at version 1.0.0)