Mass Spectrometry Standards Working Group Charter

Submitted: 2018-11-07

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 Centre Hospitalier Universitaire Vaudois (

Henry Lam, Hong Kong University of Science and Technology (



Andrew Dowsey, University of Bristol (


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

Editor(s): <position is currently unfilled>


Minimal Reporting Requirements Coordinator(s): Pierre-Alain Binz, CHUV Centre Hospitalier Universitaire Vaudois (


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
  • Development of the Universal Spectrum Identifier





Goal 1: Finish the document process for 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 2: Define and implement a Universal Spectrum Identifier (USI) that enables users, repositories, and software to universally refer to a particular spectrum across resources in a uniform manner. Foster implementation of the USI at multiple sites.


Goal 3: Define a set of common metadata and controlled vocabulary for spectral libraries and archives such that this vocabulary could be used uniformly by all existing spectral library formats. Proceed towards the ultimate deliverable of (a) new PSI spectral library/archive format(s), by first compiling a list of potential use cases, and exploring the possibility of reusing, refining and combining existing format(s).

Goal 4: Finalize mzML version 1.2 including Numpress compression of binary data and enhancements for ion mobility data. Support for compression of XML data with random access is deferred. The mzMLb format of mzML within HDF5 supports this; at the present time mzMLb is envisaged to become a parallel PSI recommended format.