@article{e778f6a506c34d99b1a5071723a46e45,
title = "Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms",
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.",
keywords = "FAIR, ProForma, data standards, file formats, mass spectrometry, peptidoform, proteoform, top-down proteomics",
author = "Leduc, {Richard D.} and Deutsch, {Eric W.} and Binz, {Pierre Alain} and Fellers, {Ryan T.} and Cesnik, {Anthony J.} and Klein, {Joshua A.} and {Van Den Bossche}, Tim and Ralf Gabriels and Arshika Yalavarthi and Yasset Perez-Riverol and Jeremy Carver and Wout Bittremieux and Shin Kawano and Benjamin Pullman and Nuno Bandeira and Kelleher, {Neil L.} and Thomas, {Paul M.} and Vizca{\'i}no, {Juan Antonio}",
note = "Funding Information: The authors would like to acknowledge all the individuals who contributed in various ways to the ProForma 2.0 specification (see specification document in the Supporting Information ). We would also like to thank the reviewers of the specification document, namely Gloria Sheynkman and Erin Jeffery (University of Virginia) and Xiaowen Liu (Tulane University School of Medicine). We are also appreciative of the contributions made by the Executive Board of the CDTP. We are especially grateful to Susan Weintraub (University of Texas Health Science Center at San Antonio) for having edited the manuscript quite extensively to make it more suitable for readers who are nonexperts in bioinformatics. This work was financially supported in part by the following: J.A.V., National Institutes of Health (R24GM127667), BBSRC (BB/S01781X/1), the EU H2020 project EPIC-XS (823839), and EMBL core funding; R.D.L., R.T.F., P.M.T., and N.L.K., National Institute of Health (P41 GM108569), the Human Biomolecular Atlas Program (UH3 CA246635), and the National Library of Medicine (R21 LM013097); S.K., the Database Integration Coordination Program from the National Bioscience Database Center, Japan Science and Technology Agency (18063028), and the Japan Society for the Promotion of Science KAKENHI (JP20H03245); A.J.C., the Knut and Alice Wallenberg Foundation (2016.0204) and the Swedish Research Council (2017-05327 to Emma Lundberg); T.V.D.B., the Research Foundation─Flanders (1S90918N); E.W.D., the National Institutes of Health (R24GM127667, R01GM087221, and U19AG023122) and the National Science Foundation (DBI-1933311); N.B., the National Institutes of Health (R24GM127667 and 1R01LM013115) and the National Science Foundation (ABI 1759980). Publisher Copyright: {\textcopyright} 2022 American Chemical Society. All rights reserved.",
year = "2022",
month = apr,
day = "1",
doi = "10.1021/acs.jproteome.1c00771",
language = "English (US)",
volume = "21",
pages = "1189--1195",
journal = "Journal of Proteome Research",
issn = "1535-3893",
publisher = "American Chemical Society",
number = "4",
}