Proteomics Informatics

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HUPO Proteomics Standards Initiative
Proteomics Informatics Working Group (PSI-PI)


  1. Group Charter
  2. Group Structure
  3. Obtaining the current Documents and Getting Involved
  4. mzIdentML
  5. mzQuantML
  6. Request new CV terms to the PSI-MS Controlled Vocabulary
  7. Meetings and Logistics
  8. Mailing List and Issue Discussion



The PSI Proteomics Informatics standards group is one of the working groups of the Proteomics Standards Initiative.


Proteomics Informatics Group Charter

At the PSI Spring Meeting in San Francisco in 2006, the PSI-PI group charter was discussed and agreed:

The PSI Proteomics Informatics (PSI-PI) standards group consists of academic, government and industry researchers, software developers, publishers and instrument manufacturers. The goals of the group are:

  • to provide a set of minimal reporting requirements which augment the MIAPE reporting guidelines with respect to analysis of data derived from proteomics experiments;
  • to provide vendor-neutral and standard formats for representing results of analyzing and processing experimental data;
  • to foster adoption of the format by highlighting efforts made by vendors and individuals that utilize the format in their products.



Group Structure (2013)

Current Encumbent
ChairAndy Jones
Co-chairMartin Eisenacher
MIAPE Co-ordinatorPierre-Alain Binz
Ontology Co-ordinatorGerhard Mayer
EditorGerhard Mayer
SecretaryJuan Antonio Vizcaino




Obtaining the Current Documents and Getting Involved

The deliverables (XML schema, example documents, specification document etc.) of the standards released by the PSI-PI working group can be found on different pages linked below.

All of the ongoing work, e.g. deliverables and issue list of the versions being under development are managed in Google Code Projects (see URLs on pages linked above!).

Google Code makes use of Subversion to allow versions of documents to be managed. You can get read-only access all of the files in subversion anonymously, or if you are a member of the group you can check out the contents of the repository, commit changes to the files and add new ones. There are many different clients that you can use to access and write to the SVN repository. If you are using Windows, the TortoiseSVN client comes highly recommended.



The main current deliverable of the Proteomics Informatics working group is the mzIdentML data exchange standard (previously known as analysisXML). Please see use cases for mzIdentML to get a flavour of its scope and purpose (mainly storing parameters and results of a spectrum identification search).

Version 1.0.0 of mzIdentML was formally released on 20th August 2009.
Work on an update to version 1.1.0 of mzIdentML was finished in August 2011.
A very minor update to version 1.1.1 was done in July 2015.

More information about mzIdentML is available HERE.

Current status of tools that write and import mzIdentML are on this page.




The other current deliverable of the Proteomics Informatics working group is the mzQuantML data exchange standard. It is intended to store parameters and results of quantification workflows.

Version 1.0.0 of mzQuantML was released in Feb 2013. More information about mzQuantML is available HERE.



Request new CV terms to the PSI-MS Controlled Vocabulary

To request new CV terms to be added to the PSI-MS Controlled Vocabulary, please use the psidev-vocab mailing list.



Meetings and Logistics

On-going communication between all participants will be achieved via the mailing list

Regularly weekly telephone conferences are organised to allow discussion of the progress and direction of the working group when appropriate. Details of the next meeting will be posted here as soon as they are available.

The group meets face to face at least once a year at the Spring PSI conference.



Mailing list and Issue Discussion

This is the discussion list for proteomics informatics (mzIdentML and mzQuantML) development.

You can subscribe to the psidev-pi-dev list.

You can view the existing posts to the psidev-pi-dev list.

To post a message to the list, send an email to