{"entity": "publication", "iuid": "512fb7ea5a584ba7bca40ee0485b966b", "timestamp": "2026-08-22T06:56:33.005Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/512fb7ea5a584ba7bca40ee0485b966b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/512fb7ea5a584ba7bca40ee0485b966b"}}, "title": "Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms.", "authors": [{"family": "LeDuc", "given": "Richard D", "initials": "RD", "orcid": "0000-0002-6951-2923", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dfae785b55854c1ea8e853e5453057af.json"}}, {"family": "Deutsch", "given": "Eric W", "initials": "EW", "orcid": "0000-0001-8732-0928", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2463c206245a4dbb979cad9d201d73c4.json"}}, {"family": "Binz", "given": "Pierre-Alain", "initials": "PA"}, {"family": "Fellers", "given": "Ryan T", "initials": "RT"}, {"family": "Cesnik", "given": "Anthony J", "initials": "AJ"}, {"family": "Klein", "given": "Joshua A", "initials": "JA"}, {"family": "Van Den Bossche", "given": "Tim", "initials": "T", "orcid": "0000-0002-5916-2587", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/01fb60460b2f47cf8883dd2f29c4f7b7.json"}}, {"family": "Gabriels", "given": "Ralf", "initials": "R", "orcid": "0000-0002-1679-1711", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/30094adc291549c28c6c74cbeb9aacd2.json"}}, {"family": "Yalavarthi", "given": "Arshika", "initials": "A"}, {"family": "Perez-Riverol", "given": "Yasset", "initials": "Y", "orcid": "0000-0001-6579-6941", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb4449bad29741b195a7593fc39a769d.json"}}, {"family": "Carver", "given": "Jeremy", "initials": "J"}, {"family": "Bittremieux", "given": "Wout", "initials": "W", "orcid": "0000-0002-3105-1359", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07e740b95ac84bb6ad8f3ff159aece03.json"}}, {"family": "Kawano", "given": "Shin", "initials": "S"}, {"family": "Pullman", "given": "Benjamin", "initials": "B"}, {"family": "Bandeira", "given": "Nuno", "initials": "N", "orcid": "0000-0001-8385-3655", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ef3073f45c14b7291348f2257d503b8.json"}}, {"family": "Kelleher", "given": "Neil L", "initials": "NL", "orcid": "0000-0002-8815-3372", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db299d87427049b8972eabe2d9f453a8.json"}}, {"family": "Thomas", "given": "Paul M", "initials": "PM"}, {"family": "Vizca\u00edno", "given": "Juan Antonio", "initials": "JA", "orcid": "0000-0002-3905-4335", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81245410f3234e658147bc94f6b3dad2.json"}}], "type": "journal article", "published": "2022-04-01", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "21", "issue": "4", "pages": "1189-1195", "issn-l": "1535-3893"}, "abstract": "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.", "doi": "10.1021/acs.jproteome.1c00771", "pmid": "35290070", "labels": [], "xrefs": [{"db": "mid", "key": "EMS144004"}, {"db": "pmc", "key": "PMC7612572"}], "notes": [], "created": "2026-08-21T11:33:58.912Z", "modified": "2026-08-21T11:33:59.098Z"}