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

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 was submitted on January, 22nd 2019 and the revised document version 1.0.0 DRAFT went through 60-days public comments and external review phase until March 25th, 2019. Following reviewer comments a revised version of the proposal was submitted on April 5th, 2019, and approved by the external reviewers on April 20th, 2019.

The document was finalized on April 23th, 2019.

A manuscript has been submitted to Journal of Proteome Research and accepted May 13th, 2019. Get it at https://doi.org/10.1021/acs.jproteome.9b00064.