PEFF in DocProc 2018 [handling editor: Sylvie Ricard-Blum]

Currently in 60-days public comments and external review phase until March 25th, 2019

There was a PEFF DocProc submission in 2008, this is a complete DocProc relaunch.

The PSI Mass Spectrometry Standards Working Group has submitted to the PSI document process a proposal for a PSI standard, the PSI Extended FASTA Format (PEFF).

An initial PEFF proposal was submitted long ago, but the suggested changes were not addressed in a timely fashion, and therefore PEFF has been submitted as a new proposal on April 3rd, 2018.  The specification document has substantial more details and supports many more features, including encoding of proteoforms, than the original submission. With the growing interest in proteogenomics, PEFF neatly addresses in a standardized manner the growing challenge of how to encode and use not just the protein sequences but also the many known annotations on those protein sequences.

The cover letter, the responses to the steering group  review, the specification document and three example files (PEFF_Tiny_Valid.peff, SmallTestDB-PEFF1.0.peff and PEFF_AnnotID_Insulin_Valid.peff) are available below and in the PEFF GitHub repository https://github.com/HUPO-PSI/PEFF.


Athough not included in this submission bundle, PEFF 1.0 files (according to the current draft specification) can already be downloaded from the neXtProt knowledge base, e.g. ftp://ftp.nextprot.org/pub/current_release/peff/
or through the web interface
https://www.nextprot.org/entry/NX_P00738/  (then select download link in upper right and choose PEFF)
https://api.nextprot.org/export/entry/NX_P00738.peff

Furthermore, software supporting PEFF is already being developed. The widely used Comet search engine supports the current draft of PEFF as described here http://comet-ms.sourceforge.net/release/release_201701/ (search on page for PEFF)
 
After having passed a 30-day review of the PSI steering group with minor changes, a revised version of the proposal has been submitted on January, 22nd 2019 and the revised document version 1.0.0 DRAFT now goes through 60-days public comments and external review phase until March 25th, 2019.

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

We invite both positive and negative comments on the relevance, correctness and clarity of the proposal (e.g. is the standard comprehensively described and are the examples in agreement with the specification?) as a whole or of specific parts of it.

Please feel free to forward this message to potentially interested colleagues. There is no requirement that people commenting should have had any prior contact with the PSI.  

Please send comments by e-mail to sylvie.ricard-blum@univ-lyon1.fr.

Thank you very much in advance.