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. A standard notation for proteoforms and peptidoforms is then required for the community, so that it can be embedded in many relevant PSI (and potentially other) file formats.
The PSI has developed a format called PEFF (PSI Extended FASTA Format, http://www.psidev.info/peff) that can be used to represent proteoforms. Additionally, the Consortium for Top Down Proteomics (CTDP) developed a notation format called ProForma (https://topdownproteomics.github.io/ProteoformNomenclatureStandard/), aiming to represent proteoforms.
This format specification represents the consortium reached by both groups in order to standardise the representation of proteoforms/peptidoforms supporting the main proteomics approaches, including both bottom-up (focused on peptides/peptidoforms) and top down (focused on proteins/proteoforms) approaches.
More information is available at: https://github.com/HUPO-PSI/ProForma/.
The current version of the specification document (both in PDF and Word format) is available at:
https://github.com/HUPO-PSI/ProForma/tree/master/SpecDocument.
Proforma v2 in DocProc [handling editor: Sylvie Ricard-Blum]
The specification document, ProForma (Proteoform and Peptidoform Notation (version 2.0.0, draft 12) has been submitted to the PSI document process.
After having passed a 30-day review of the PSI steering group with minor changes, the proposed document version 2.0.0 DRAFT now goes through 60-day public comments and external review phase until February 27th, 2021.
ProForma v2 aims to standardise the representation of proteoforms/peptidoforms supporting the main proteomics approaches, including both bottom-up (focused on peptides/peptidoforms) and top down (focused on proteins/proteoforms) approaches.
Specification document: ProForma_v2_draft12_0.docx, ProForma_v2_draft12_0.pdf
Use case examples: https://github.com/HUPO-PSI/ProForma/
Development background: https://github.com/HUPO-PSI/ProForma
Please send comments by e-mail directly to sylvie.ricard-blum at univ-lyon1.fr
for example regarding the following criteria:
- That the specification is presented in accordance with the templates and is clearly written.
- That it is sufficiently detailed and comprehensively describes the necessary and sufficient explanation of the specification.
If you do not feel experienced enough to comment on this document, but know colleagues who are, please consider forwarding this request to them.
There is no requirement that people commenting should have had any prior contact with the PSI.
Thank you very much in advance for your valuable time and participation
Sylvie RICARD-BLUM - PSI Editor