PSI Editors

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).

MIAPE-MS in DocProc (Update type b) [handling editor: Martin Eisenacher]

The MIAPE-MS work group has submitted some changes for the
MIAPE-MS document after review feedback (comments and answers attached).
As these were minor changes, a new public review phase is not necessary.
As there were no further comments until 7th August 2012, the document status changed to "Final" (announced 15th August 2012).

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

MIAPE Quant in DocProc [handling editors: Christian Stephan / Martin Eisenacher]

Submission of Major Revision :

After considering the comments of one public and two invited reviewers attached is a revised version 0.9.2_RC of MIAPE-Quant (plus answers to reviewers and updated examples). 

It goes through two weeks of further review, which will be viewed and editored after 8th October 2012. Please send any comments about the changes to or add comments to this page.

Major Revision accepted on 18th October 2012; Final version 1.0 published on 24th October 2012).