[Psidev-qc-dev] HUPO-PSI Specification mzIdentML version 1.3.0 + crosslinking extension 45-day public review

[Sylvie R. <syl...@un...>]

Dear colleagues, dear members of the HUPO-PSI community,

The HUPO Proteomics Standards Initiative (PSI) develops standards  for 
documentation and storage of Proteomics data (see http://www.psidev.info 
for an overview of activities).

The PSI Proteomics Informatics Working Group has submitted a new 
recommendation for consideration and review as a PSI standard. The 
mzIdentML document, draft of version 1.3.0, defines an XML schema that 
can be used to describe the outputs of proteomics search engines or 
similar software for peptide/protein identification from mass 
spectrometry(MS) data with an extension document for the identification 
of crosslinked peptides.

After having been reviewed by the PSI steering group and revised as 
requested by an internal reviewer, the proposed documents, mzIdentML 
draft of version 1.3.0 and the crosslinking extension document, now go 
through the 45-day public and external review until*April 8^th , 2024*.

The mzIdentML document (draft of version 1.3.0), a word document 
tracking changes from version 1.2.0, the crosslinking extension 
document, and the example files are available on GitHub as detailed below.

*The mzIdentML document version 1.3.0, draft *
https://github.com/HUPO-PSI/mzIdentML/blob/master/specification_document/specdoc1_3-draft/mzIdentML1.3.0-draft_vJuly2023.pdf

*A word document tracking changes from version 1.2.0*
https://github.com/HUPO-PSI/mzIdentML/blob/master/specification_document/specdoc1_3-draft/mzIdentML1.3.0-draft_vJuly2023_CC3%20JAV.docx

*The crosslinking extension document*
https://github.com/HUPO-PSI/mzIdentML/blob/master/specification_document/specdoc1_3-draft/mzIdentML%201.3.0%20Crosslinking%20Extension.pdf

*The example files*
https://github.com/HUPO-PSI/mzIdentML/tree/master/examples/1_3examples/crosslinking

*The pre-print*is available at 
https://www.authorea.com/users/672647/articles/671627-mzidentml 
-1-3-0-essential-progress-on-the-support-of-crosslinking-and-other-identifications-based-on-multiple-spectra

This message is to encourage you to contribute to the standards 
development activity by commenting on the documents. We invite both 
positive and negative comments on the relevance, correctness, clarity 
and appropriateness of the specification (e.g. is it presented in 
accordance with the templates and clearly written, is it sufficiently 
detailed and comprehensively described and are the examples in agreement 
with the specification?). Comments can be made on the specification as a 
whole or on specific parts.

If you do not feel experienced enough to comment on this document, but 
know colleagues who are, please feel free to forward this message to 
them. There is no requirement that people commenting should have had any 
prior contact with the PSI.

Please send your comments by e-mail directly to 
syl...@un... before*April 8th, 2024*.

Thank you very much in advance for your help in improving PSI standards.

Best wishes.

Professor Sylvie RICARD-BLUM - PSI Editor
Pericellular and Extracellular Supramolecular Assemblies
UMR 5246 CNRS - University Lyon 1
Institute of Molecular and Supramolecular Chemistry and Biochemistry
University Claude Bernard Lyon 1, 43 Boulevard du 11 novembre 1918
69622 Villeurbanne Cedex, France
Phone: +33(0)4 72 44 82 32
E-mail: syl...@un...