Steering Committee

Proforma v2

Protein and peptide sequences are usually represented using a string of amino acids using a well-known one letter code endorsed by the IUPAC. However, there is still no clear consensus about how to represent ‘proteoforms’ and ‘peptidoforms’, meaning all possible variations of a protein/peptide sequence, including protein modifications, both artefactual and post-translational modifications (PTMs). There are indeed multiple ways of encoding mass modifications and extended discussion has taken place to achieve a consensus.

Universal Spectrum Identifier in DocProc [handling editor: Martin Eisenacher]

3.) Standard final

After implementation of remaining changes standard was finalized as version 1.0.0 on July 22nd, 2021.

2.) Resubmission and check by invited and public reviewers

The author addressed comments of invited and public reviewers, resubmitted the spec doc., all reviewers checked the changes and commented again, editor requested some minor changes (see PSI editor notes): July 15th, 2021.

1.) Original submission (after steering group review)

PSI-MI XML 3.0.0 in DocProc [handling editor: Martin Eisenacher]

2.) Resubmission
After synchronized journal publication the specification document has been resubmitted on April 18th, 2018 and comments requesting changes by the three reviewers have been checked by the editor.

Document was finalized on April 5th, 2018.


1.) Original submission (after steering group review)

There has been a submission to the PSI Document Process by the Molecular Interactions workgroup updating the PSI-MI format to version 3.0.0 (from long-time stable XML 2.5, released 2005).

mzTab in DocProc [handling editor: Martin Eisenacher]

8.) Suggestion after Editor Approval:

After inspection of changes (see comments in "R4_Answers_to_Reviewers_PSI_mzTab_R3_with_comments_of_PSI_editor.docx" file) recommendation to the steering committee on August 20th, 2014: accept the mzTab specification R4 without further changes.
September, 2nd, 2014: acceptance. Final version 1.0.0. was announced September 15th, 2014.

7.) Submission of revised version R4

mzQuantML in DocProc (original version 1.0.0-rc1 [acting handling editor: Pierre-Alain Binz]

Original submission:

This document defines an XML schema that can be used to describe the outputs of quantification software for proteomics (quantitative values about peptides and proteins) and potentially metabolomics (quantitative values about small molecules), derived from analysis of mass spectrometry data.

All example files can be downloaded manually from:

mzQuantML 1.0.1 in DocProc [handling editor: Martin Eisenacher]

A modififed specification of the mzQuantML recommendation document was submitted to the PSI document process including the encoding of SRM quantification results. After careful consideration and discussion with the submitters I think it is minor and therefore version 1.0.1 (if you disagree, especially if existing software is made incompatible, please give me a note).

Please review the updated specification document below WITHIN TWO WEEKS and send any corrections or comments until April 12th to the handling editor martin.eisenacher<AT>

proBed in DocProc [handling editor: Martin Eisenacher]

acceptance: final version 1.0.0 as of March 13th, 2017 (was announced April 13th, 2017)

3.) R1 submission

The attached documents are a revised submission of the Recommendation Document for the file format "proBed". A "responses to reviewers" document is also included. This now goes through a 14-days review phase (public and already invited reviewers, end: 13th March 2017) .

2.) Suggestion after receiving invited and public reviews: