Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms.
Journal of proteome research
washington; isb; seattle; genomics; Humans; Protein Processing, Post-Translational; Proteome; Proteomics; Reference Standards; Software
It is important for the proteomics community to have a standardized manner to represent all possible variations of a protein or peptide primary sequence, including natural, chemically induced, and artifactual modifications. The Human Proteome Organization Proteomics Standards Initiative in collaboration with several members of the Consortium for Top-Down Proteomics (CTDP) has developed a standard notation called ProForma 2.0, which is a substantial extension of the original ProForma notation developed by the CTDP. ProForma 2.0 aims to unify the representation of proteoforms and peptidoforms. ProForma 2.0 supports use cases needed for bottom-up and middle-/top-down proteomics approaches and allows the encoding of highly modified proteins and peptides using a human- and machine-readable string. ProForma 2.0 can be used to represent protein modifications in a specified or ambiguous location, designated by mass shifts, chemical formulas, or controlled vocabulary terms, including cross-links (natural and chemical) and atomic isotopes. Notational conventions are based on public controlled vocabularies and ontologies. The most up-to-date full specification document and information about software implementations are available at http://psidev.info/proforma.
Institute for Systems Biology
LeDuc, Richard D; Deutsch, Eric W; Binz, Pierre-Alain; Fellers, Ryan T; Cesnik, Anthony J; Klein, Joshua A; Van Den Bossche, Tim; Gabriels, Ralf; Yalavarthi, Arshika; Perez-Riverol, Yasset; Carver, Jeremy; Bittremieux, Wout; Kawano, Shin; Pullman, Benjamin; Bandeira, Nuno; Kelleher, Neil L; Thomas, Paul M; and Vizcaíno, Juan Antonio, "Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms." (2022). Articles, Abstracts, and Reports. 5887.