mzTab in DocProc [handling editor: Martin Eisenacher]

Description: 

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

June 20th, 2014: The submitted documents contain changes due to PSI DocProc reviewers and Journal reviewers. As DocProc changes were minor, PSI editor assessed them (together with changes due to journal reviewers) without further sent-out (find information about the original submission and previous re-submissions below).

6.) Suggestion after 30-days external review and public comments phase:

Comments have been received about R3 from one external invited reviewer and three of the previous commenters. Recommendation to steering commitee on April 4th, 2014: Minor revision, then wait for changes due to journal reviewers, then Final after Editor Approval.

5.) Submission of revised version R3:

These documents are a revision of the Recommendation Document for the file format "mzTab" after public and invited review (find information about the original submission and previous re-submissions below).

After previous review steps and an unforeseen major restructuring ("identification / quantification" type, "summary / complete" detail level) the proposed document version 1.0, release candidate 5 (file name prefix R3) now goes through 30-days public comments phase (starting after christmas break, end: 14th February 2014). Also previous commenters will be asked to review the changes. (Due to the unforeseen restructuring the previous judgement "Final after Editor approval" had to be modified.)

The public comment period enables the wider community to provide feedback on a proposed standard before it is formally accepted, and thus is an important step in the standardisation process.

Attached are the R3 format specification document (doc and PDF), the R2-R3-DIFF doc, the 20 minutes guide to mzTab (doc and PDF), the answers to reviewers comments, plus the updated corresponding example files (without MaxQuant_SILAC due to file size). All example files can be found here.

Please add comments (or send them directly to martin.eisenacher: at : rub.de) especially those related to the incorporated changes.

4.) Suggestion after 14-days external and public review phase:

Comments have been received about R2 from two external invited reviewers, one steering commitee member and four public commenters. Suggestion to steering commitee on April 3rd, 2013: Very minor changes, then Final after Editor Approval. (December 23rd, 2013: due to major changes of the document, Editor Approval is not sufficient (see Submission of revised version R3 above)

3.) Submission of revised version R2:

These documents are a revision of the Recommendation Document for the file format "mzTab" after public and invited review
(find information about the original submission below).

After steering committee review and major changes following the public and external review phase
the proposed document version 1.0, release candidate 2 (file name prefix R2) now goes through shortened
14-days public comments phase (end: 24th March 2013). Also previous commenters will be asked to review the changes.

The public comment period enables the wider community to provide feedback on a proposed standard before it is formally accepted,
and thus is an important step in the standardisation process.

Attached are the R2 Cover Letter, the specification documents in Word and PDF format plus
the updated corresponding example files (zipped in two portions, one of which containing one .gz file).

Please add comments (or send them directly to martin.eisenacher: at : rub.de) especially those
related to the incorporated changes.

2.) Suggestion after external and public review phase:

Comments have been received from two external invited reviewers, one steering commitee member and two public commenters. Suggestion to steering commitee on November 6th, 2012: major changes.

1.) Original submission:

These documents are a new submission of the Recommendation Document for the file format "mzTab".

"mzTab is intended as a lightweight supplement to the already existing standard file formats mzIdentML and mzQuantML, providing a summary of the final results of a MS-based proteomics experiment. mzTab files can contain protein, peptide, and small molecule identifications together with basic quantitative information and supports different levels of metadata reporting." (see also Cover Letter attached)

It is important to highlight again that mzTab is not intended to store an experiment’s complete data / evidence but only its final reported results.

After having passed a 30-day review of the PSI steering commitee with minor formal changes, the proposed document version 1.0 release candidate now goes through 60-days public comments and external review phase (end: 12th October 2012, prolonged to 26th October).

The public comment period enables the wider community to provide feedback on a proposed standard before it is formally accepted, and thus is an important step in the standardisation process.

Attached are the mzTab Cover Letter, the specification documents in Word and PDF format plus the corresponding example files (zipped, current versions can also be accessed at http://code.google.com/p/mztab/wiki/ExampleFiles). The '10 min guide to mzTab' document is a tutorial-like "first-steps" description of the format.

Please add comments (or send them directly to martin.eisenacher: at : rub.de) for example regarding the following criteria:

  1. That it is well formed – that is, it is presented in accordance with the templates and is clearly written.
  2. That it is sufficiently detailed and clearly contains and comprehensively describes the necessary and sufficient explanation of the format.
  3. That the examples are in accordance with the specification.

This message is to encourage you to contribute to the standards development activity by commenting on the material that is available online. We invite both positive and negative comments. If negative comments are being made, these could be on the relevance, clarity, correctness, appropriateness, etc, of the proposal as a whole or of specific parts of the proposal.

If you do not feel well placed to comment on this document, but know someone who may be, please consider forwarding this request. There is no requirement that people commenting should have had any prior contact with the PSI.

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