The steering committee is a group of volunteers who organise the activities of the HUPO-PSI - see here for details.
HUPO Proteomics Standards Initiative
HUPO Proteomics Standards Initiative - Protein Separation Workgroup (PSI-PS)
The group has been formed following a merger of the PSI-GEL and SP (sample processing and separations) workgroups
PS Group Charter
PSI editors manage the document process and the communication between external reviewers, the public and the steering commitee.
Current PSI editors:
Sylvie Ricard-Blum, Univ. Lyon (sylvie.ricard-blum :at: univ-lyon1.fr)
Martin Eisenacher, Ruhr-Univ. Bochum (martin.eisenacher :at: rub.de)
Reporting guidelines for proteomics
The context-sensitive nature of transcriptome, metabolome and proteome data necessitates the capture of a richer set of metadata (data about the data) than is required for basic genetic sequence, where usually knowing the organism of origin will suffice. The use of paper citations as proxies for actual metadata hinders the reassessment of data sets, and obstructs non-standard searching (e.g.
PSI-MI XML3.0 has now been through community review and is being prepared for publication. Please access on
- MIF300.xsd: https://github.com/HUPO-PSI/miXML/blob/master/3.0/src/MIF300.xsd
- MIF300 schema documentation : https://rawgit.com/HUPO-PSI/miXML/master/3.0/doc/MIF300.html
The Molecular Interactions workgroup is concentrating on:
PSI-MS: Mass Spectrometry Standards Working Group
| Controlled vocabulary development | Email discussion list |
The PSI-MSS working group defines community data formats and controlled vocabulary terms facilitating data exchange and archiving in the the field of proteomics mass spectrometry.
Current projects are:
- The mzML format, which merges the mzData format (see below) and another similar format mzXML. mzML 1.1.0 was released on June 1, 2009 and has been stable since then. Everyone is encouraged to implement mzML 1.1.0 in their software. See the mzML information page for the full specification, other documentation and examples.
- The TraML format has been developed as a standardized format for the exchange and transmission of transition lists for selected reaction monitoring (SRM) experiments. This specification has been been accepted through the PSI document process and is complete. Please email the list email@example.com with your questions, comments, and suggestions. See the TraML information page for the full specification, other documentation and examples.
Past achievements are:
- The mzData standard, which captures mass spectrometry output data. mzData's aim is to unite the large number of current formats (pkl's, dta's, mgf's, .....) into a single format. mzData has been released and is stable at version 1.05. It is now deprecated in favor of mzML.
|Chair||Eric Deutsch, Institute for Systems Biology|
Pierre-Alain Binz, Centre Universitaire Hospitalier Vaudois CHUV
Henry Lam, Hong Kong University of Science and Technology
Andrew Dowsey, University of Bristol
|MIAPE||Pierre-Alain Binz, Centre Universitaire Hospitalier Vaudois CHUV|
Gerhard Mayer, Ruhr-University Bochum
As of 2006 there existed two separate XML formats for encoding raw spectrometer output: mzData developed by the PSI and mzXML developed at the Seattle Proteome Center at the Institute for Systems Biology. It is recognized that the existence of two separate formats for essentially the same thing generates confusion and extra programming effort. Therefore the PSI, with full participation by ISB, developed a new format intended to replace the previous two formats, by merging the best ideas from each format. This new format is called mzML. See the information page for mzML which includes current documentation, example files and other related materials. We encourage everyone to implement mzML in their software and workflows and cease using mzXML and mzData as soon as possible.
The mzData standard
mzData in a nutshell
Technical description and other resources
Questions? Consult the PSI-MS email discussion list
You can mail to this list at firstname.lastname@example.org, or subscribe/unsubscribe.
Last edited by: Pierre-Alain Binz 2014-04-09