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PSI-MS: Mass Spectrometry Standards Working Group

Submitted by webmaster on Mon, 2006-10-09 13:20.


PSI-MS: Mass Spectrometry Standards Working Group

About us

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.

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 (below).

Current projects are:

  • The mzML format, which merges the mzData format and another similar format mzXML. mzML 1.1.0 was released on June 1, 2009. 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 is being developed as a standardized format for the exchange and transmission of transition lists for selected reaction monitoring (SRM) experiments. This specification is still in an early draft form and feedback is actively desired. Please email the list psidev-ms-dev@lists.sourceforge.net with your comments and suggestions. See the TraML information page for the full specification, other documentation and examples.

Note that the mzIndentML (formerly AnalysisXML) format now comes under the aegis of the Proteomics Informatics Working Group.

Group Structure (2009)

Role

Name

Chair Eric Deutsch, Institute for Systems Biology
Co-chair Pierre-Alain Binz, Swiss Institute of Bioinformatics and GeneBio

Secretary

Lennart Martens, European Bioinformatics Institute
MIAPE Pierre-Alain Binz, Swiss Institute of Bioinformatics and GeneBio
Ontology Co-ordinators

Marc Sturm, University of Tubingen

Darren Kessner, Cedars-Sinai Medical Center

Matthew Chambers, Vanderbilt University

Fredrik Levander, Lund University

Randy Julian, Indigo Biosystems

Luisa Montecchi-Palazzi, European Bioinformatics Institute

Jim Shofstahl, Thermo Fisher Scientific
Other Working Group Members:
 Steffen Neumann, IPB Halle
 David Creasy, Matrix Science Ltd.
 Wilfred Tang, Applied Biosystems
 Phil Jones, European Bioinformatics Institute
 Pete Souda, University of California, Los Angeles
 Ruth McNally, ESRC CESAGen
 Patrick Pedrioli, Swiss Institute of Technology
 Angel Pizarro, University of Pittsburgh
 Sean Seymour, Applied Biosystems
 Jayson Falkner, University of Michigan
 Natalie Tasman, Insilicos
 David Horn, Agilent Technologies
 Liming Yang, NIH/NCI
 


mzML Standard 

Status: Released 1.1.0 [more information...]

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 stop using mzXML and mzData as soon as possible.

 


TraML Standard 

Status: Early draft form 0.2.0  [more information...]

The HUPO PSI Mass Spectrometry Standards Working Group (MSS WG) has begun developing a draft specification for a standardized format for the exchange and transmission of transition lists for selected reaction monitoring (SRM) experiments. This specification is still in an early draft form and feedback is actively desired. Please email the list psidev-ms-dev@lists.sourceforge.net with your comments and suggestions. See the information page for TraML which includes current documentation, example files and other related materials.


The mzData standard

Status: version 1.05. Deprecated.

mzData in a nutshell

mzData is a data format capturing peak list information. Its aim is to unite the large number of current formats (pkl's, dta's, mgf's, .....) into one; mzData. mzData is NOT a substitute for the rawfile formats of the instrument vendors. Some vendors, if not all, will provide software transforming their raw files to mzData. There are already a number of programs which can use mzData. In order to keep the filesize of mzData limited, mz/intensity information is stored in "binary base 64 format".

Technical description and other resources

Questions? Consult the PSI-MS email discussion list

 



Moderated email discussion list

 

We also provide a mail discussion list for mass spectroscopy standard development.
You can mail to this list at psidev-ms-dev@lists.sourceforge.net, browse the archive, or subscribe/unsubscribe.

Last edited by: Eric Deutsch 2009-02-17


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