Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms br

It is important for the proteomics community to have a standardizedmanner to represent all possible variations of a protein or peptide primary sequence,including natural, chemically induced, and artifactual modifications. The HumanProteome Organization Proteomics Standards Initiative in collaboratio...

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Bibliographic Details
Published in:Journal of proteome research 2022, Vol.21 (4), p.1189
Main Authors: 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., Vizcaino, Juan Antonio
Format: Article
Language:English
Subjects:
data standards
FAIR
file formats
mass spectrometry
peptidoform
ProForma
proteoform
top-down proteomics
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Summary:It is important for the proteomics community to have a standardizedmanner to represent all possible variations of a protein or peptide primary sequence,including natural, chemically induced, and artifactual modifications. The HumanProteome Organization Proteomics Standards Initiative in collaboration with severalmembers of the Consortium for Top-Down Proteomics (CTDP) has developed astandard notation called ProForma 2.0, which is a substantial extension of the originalProForma notation developed by the CTDP. ProForma 2.0 aims to unify therepresentation of proteoforms and peptidoforms. ProForma 2.0 supports use casesneeded for bottom-up and middle-/top-down proteomics approaches and allows theencoding 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 bymass 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 documentand information about software implementations are available athttp://psidev.info/proforma.
ISSN:1535-3907
1535-3893
DOI:10.1021/acs.jproteome.1c00771