  There is the need to represent in a standard manner all the possible
variations of a protein or peptide primary sequence, including both artefactual
and post-translational modifications of peptides and proteins. With that
overall aim, here, the Human Proteome Organization (HUPO) Proteomics Standards
Initiative (PSI) has developed a notation, called ProForma 2.0, which is a
substantial extension of the original ProForma notation, developed by the
Consortium for Top-Down Proteomics (CTDP). ProForma 2.0 aims to unify the
representation of proteoforms and peptidoforms. Therefore, this notation
supports use cases needed for bottom-up and middle/topdown proteomics
approaches and allows the encoding of highly modified proteins and peptides
using a human and machine-readable string. ProForma 2.0 covers encoding protein
modification names and accessions, cross-linking reagents including disulfides,
glycans, modifications encoded using mass shifts and/or via chemical formulas,
labile and C or N-terminal modifications, ambiguity in the modification
position and representation of atomic isotopes, among other use cases.
Notational conventions are based on public controlled vocabularies and
ontologies. Detailed information about the notation and existing
implementations are available at http://www.psidev.info/proforma and at the
corresponding GitHub repository (https://github.com/HUPO-PSI/proforma).
