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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 (UGent) , Ralf Gabriels (UGent) , Arshika Yalavarthi, Yasset Perez-Riverol, et al.
(2022) JOURNAL OF PROTEOME RESEARCH. 21(4). p.1189-1195
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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
ProForma, proteoform, peptidoform, top-down proteomics, file formats, data standards, mass spectrometry, FAIR

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MLA
LeDuc, Richard D., et al. “Proteomics Standards Initiative’s ProForma 2.0 : Unifying the Encoding of Proteoforms and Peptidoforms.” JOURNAL OF PROTEOME RESEARCH, vol. 21, no. 4, 2022, pp. 1189–95, doi:10.1021/acs.jproteome.1c00771.
APA
LeDuc, R. D., Deutsch, E. W., Binz, P.-A., Fellers, R. T., Cesnik, A. J., Klein, J. A., … 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
Chicago author-date
LeDuc, Richard D., Eric W. Deutsch, Pierre-Alain Binz, Ryan T. Fellers, Anthony J. Cesnik, Joshua A. Klein, Tim Van Den Bossche, et al. 2022. “Proteomics Standards Initiative’s ProForma 2.0 : Unifying the Encoding of Proteoforms and Peptidoforms.” JOURNAL OF PROTEOME RESEARCH 21 (4): 1189–95. https://doi.org/10.1021/acs.jproteome.1c00771.
Chicago author-date (all authors)
LeDuc, Richard D., 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, and Juan Antonio Vizcaíno. 2022. “Proteomics Standards Initiative’s ProForma 2.0 : Unifying the Encoding of Proteoforms and Peptidoforms.” JOURNAL OF PROTEOME RESEARCH 21 (4): 1189–1195. doi:10.1021/acs.jproteome.1c00771.
Vancouver
1.
LeDuc RD, Deutsch EW, Binz P-A, Fellers RT, Cesnik AJ, Klein JA, et al. Proteomics standards initiative’s ProForma 2.0 : unifying the encoding of proteoforms and peptidoforms. JOURNAL OF PROTEOME RESEARCH. 2022;21(4):1189–95.
IEEE
[1]
R. D. LeDuc et al., “Proteomics standards initiative’s ProForma 2.0 : unifying the encoding of proteoforms and peptidoforms,” JOURNAL OF PROTEOME RESEARCH, vol. 21, no. 4, pp. 1189–1195, 2022.
@article{8769353,
  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.}},
  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 Gabriels, Ralf and Yalavarthi, Arshika and Perez-Riverol, Yasset and Carver, Jeremy and Bittremieux, Wout and Kawano, Shin and Pullman, Benjamin and Bandeira, Nuno and Kelleher, Neil L. and Thomas, Paul M. and Vizcaíno, Juan Antonio}},
  issn         = {{1535-3893}},
  journal      = {{JOURNAL OF PROTEOME RESEARCH}},
  keywords     = {{ProForma,proteoform,peptidoform,top-down proteomics,file formats,data standards,mass spectrometry,FAIR}},
  language     = {{eng}},
  number       = {{4}},
  pages        = {{1189--1195}},
  title        = {{Proteomics standards initiative’s ProForma 2.0 : unifying the encoding of proteoforms and peptidoforms}},
  url          = {{http://doi.org/10.1021/acs.jproteome.1c00771}},
  volume       = {{21}},
  year         = {{2022}},
}
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