Mass Spectrometry Standards Working Group Charter

Submitted: 2016-06-10

Template Rev2016b


1.Administrative Section

 Status (New/Update): Update

 Group Name:

A group name should be reasonably descriptive or identifiable.  Additionally, the group must define an acronym (maximum of 8 printable ASCII characters) to reference the group in the PSI directories, mailing lists, and general documents.  The name and acronym must not conflict with any other PSI name and acronym.

HUPO PSI Mass Spectrometry Standards Working Group (PSI-MS WG)


Chair (with affiliation and current email address):

Eric Deutsch, Institute for Systems Biology (


Co-Chairs (1 or 2) (with affiliation and current email address):

Pierre-Alain Binz, CHUV ( 


<position is currently unfilled>


Other officers (optional) (with affiliation and current email address):

Editor(s): <position is currently unfilled>

Minimal Reporting Requirements Coordinator(s): Pierre-Alain Binz, CHUV


Ontology Coordinator(s): Gerhard Mayer, Ruhr-University Bochum (

Web site Maintainer(s): <position is currently unfilled> 

Mailing list:

2.Description and objectives 

Focus and Purpose

The PSI-MS working group is composed of academic, government, and industry researchers, software developers, journal representatives, and instrument manufacturers. The main goal of the PSI-MS working group is to define community data formats and associated controlled vocabulary terms, facilitating data exchange and archiving of mass spectrometry raw data and other data needed as input to informatics analysis.

Current projects of the PSI-MS working group are:

  • Ongoing maintenance and enhancement of the mzML format

  • Completion of the PEFF format

  • Definition of a common set of spectral library/archive metadata



Goal 1: Complete an implementation of the blocked zip algorithm for mzML. The blocked zip algorithm, borrowed from the genomics field, enables random access into a zipped file. This would allow mzML files to remain zipped, which still easily allowing for sequential and random access, along with standard unzipping for complete backwards compatibility.

Goal 2: Complete and submit to the document process the PEFF (PSI Extended FASTA Format). This format is an enhancement of the FASTA format, with the important extension for reliable parsing of the description entries. PEFF files are mostly backwards compatible with FASTA, with the exceptions that FASTA parsers that do not skip lines beginning with # and those that do not handle very long description lines gracefully may have difficulties. 

Goal 3: Define a set of common metadata and controlled vocabulary for spectral libraries and archives. Although there is not currently enough momentum in defining a new PSI spectral library format, there is enough enthusiasm for creating a set of common terms for encoding spectral library and spectrum metadata, such that it could be used uniformly along with any of the existing spectral library or spectral archive formats.