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

Richard D. Leduc; Eric W. Deutsch; Pierre Alain Binz; Ryan T. Fellers; Anthony J. Cesnik; Joshua A. Klein; Tim Van Den Bossche; Ralf Gabriels; Arshika Yalavarthi; Yasset Perez-Riverol; Jeremy Carver; Wout Bittremieux; Shin Kawano; Benjamin Pullman; Nuno Bandeira; Neil L. Kelleher; Paul M. Thomas; Juan Antonio Vizcaíno

doi:10.1021/acs.jproteome.1c00771

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

Richard D. Leduc, Eric W. Deutsch, Pierre Alain Binz, Ryan T. Fellers, Anthony J. Cesnik, Joshua A. Klein, Tim Van Den Bossche, Ralf Gabriels, Arshika Yalavarthi, Yasset Perez-Riverol, Jeremy Carver, Wout Bittremieux, Shin Kawano, Benjamin Pullman, Nuno Bandeira, Neil L. Kelleher, Paul M. Thomas, Juan Antonio Vizcaíno

Résultats de recherche: Contribution à un journal › Article › Revue par des pairs

17 Citations (Scopus)

Résumé

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.

langue originale	Anglais
Pages (de - à)	1189-1195
Nombre de pages	7
journal	Journal of Proteome Research
Volume	21
Numéro de publication	4
Les DOIs	https://doi.org/10.1021/acs.jproteome.1c00771
état	Publié - 1 avr. 2022
Modification externe	Oui

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10.1021/acs.jproteome.1c00771

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Leduc, R. D., Deutsch, E. W., Binz, P. A., Fellers, R. T., Cesnik, A. J., Klein, J. A., Van Den Bossche, T., Gabriels, R., Yalavarthi, A., Perez-Riverol, Y., Carver, J., Bittremieux, W., Kawano, S., Pullman, B., Bandeira, N., Kelleher, N. L., Thomas, P. M., & Vizcaíno, J. A. (2022). Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms. Journal of Proteome Research, 21(4), 1189-1195. https://doi.org/10.1021/acs.jproteome.1c00771

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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.",

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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}",

year = "2022",

month = apr,

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doi = "10.1021/acs.jproteome.1c00771",

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Leduc, RD, Deutsch, EW, Binz, PA, Fellers, RT, Cesnik, AJ, Klein, JA, Van Den Bossche, T, Gabriels, R, Yalavarthi, A, Perez-Riverol, Y, Carver, J, Bittremieux, W, Kawano, S, Pullman, B, Bandeira, N, Kelleher, NL, Thomas, PM & Vizcaíno, JA 2022, 'Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms', Journal of Proteome Research, VOL. 21, Numéro 4, p. 1189-1195. https://doi.org/10.1021/acs.jproteome.1c00771

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AU - Deutsch, Eric W.

AU - Binz, Pierre Alain

AU - Fellers, Ryan T.

AU - Cesnik, Anthony J.

AU - Klein, Joshua A.

AU - Van Den Bossche, Tim

AU - Gabriels, Ralf

AU - Yalavarthi, Arshika

AU - Perez-Riverol, Yasset

AU - Carver, Jeremy

AU - Bittremieux, Wout

AU - Kawano, Shin

AU - Pullman, Benjamin

AU - Bandeira, Nuno

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AU - Thomas, Paul M.

AU - Vizcaíno, Juan Antonio

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KW - mass spectrometry

KW - peptidoform

KW - proteoform

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