TraML 1.0.0 Specification

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 psidev-ms-dev@lists.sourceforge.net with your questions, comments, and suggestions.


TraML Development Timeline

(updated 2013-04-22)

  • 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

(updated 2013-04-22)

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)

 

Documentation files:

- Full Specification Document: TraML1.0.0.0_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 (from CVS shared with mzML) 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.

- A definition of ontologies can be found in ontologies.xml

 

Sample instance documents for all relevant formats:

- ToyExample1.TraML

- Yeast_ATAQS_gen.TraML (6 MB)

- Yeast_InclusionList.TraML

 - xcmsIncludeTest.TraML

 - TSQ_1832_jTraML_converted.TraML
 

 

Other resources:

 - 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)

 

Older historical documents:

- Response to the reviewer comments from initial PSI document process submission (updated 2011-10-06)

- ASMS June 2009 Poster (3MB PPT)

 

 

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