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Proteomics standards initiatives ProForma 2.0 unifying the encoding of proteoforms and peptidoforms

(2021) ARXIV.
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Abstract
There is the need to represent in a standard manner all the possible variations of a protein or peptide primary sequence, including both artefactual and post-translational modifications of peptides and proteins. With that overall aim, here, the Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has developed a notation, called ProForma 2.0, which is a substantial extension of the original ProForma notation, developed by the Consortium for Top-Down Proteomics (CTDP). ProForma 2.0 aims to unify the representation of proteoforms and peptidoforms. Therefore, this notation supports use cases needed for bottom-up and middle/topdown proteomics approaches and allows the encoding of highly modified proteins and peptides using a human and machine-readable string. ProForma 2.0 covers encoding protein modification names and accessions, cross-linking reagents including disulfides, glycans, modifications encoded using mass shifts and/or via chemical formulas, labile and C or N-terminal modifications, ambiguity in the modification position and representation of atomic isotopes, among other use cases. Notational conventions are based on public controlled vocabularies and ontologies. Detailed information about the notation and existing implementations are available at http://www.psidev.info/proforma and at the corresponding GitHub repository (https://github.com/HUPO-PSI/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 Initiatives ProForma 2.0 Unifying the Encoding of Proteoforms and Peptidoforms.” ARXIV, 2021.
APA
LeDuc, R. D., Deutsch, E. W., Binz, P.-A., Fellers, R. T., Cesnik, A. J., Klein, J. A., … Vizcaíno, J. A. (2021). Proteomics standards initiatives ProForma 2.0 unifying the encoding of proteoforms and peptidoforms. ARXIV.
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. 2021. “Proteomics Standards Initiatives ProForma 2.0 Unifying the Encoding of Proteoforms and Peptidoforms.” ARXIV.
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. 2021. “Proteomics Standards Initiatives ProForma 2.0 Unifying the Encoding of Proteoforms and Peptidoforms.” ARXIV.
Vancouver
1.
LeDuc RD, Deutsch EW, Binz P-A, Fellers RT, Cesnik AJ, Klein JA, et al. Proteomics standards initiatives ProForma 2.0 unifying the encoding of proteoforms and peptidoforms. ARXIV. 2021.
IEEE
[1]
R. D. LeDuc et al., “Proteomics standards initiatives ProForma 2.0 unifying the encoding of proteoforms and peptidoforms,” ARXIV. 2021.
@misc{8727457,
  abstract     = {{There is the need to represent in a standard manner all the possible variations of a protein or peptide primary sequence, including both artefactual and post-translational modifications of peptides and proteins. With that overall aim, here, the Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has developed a notation, called ProForma 2.0, which is a substantial extension of the original ProForma notation, developed by the Consortium for Top-Down Proteomics (CTDP). ProForma 2.0 aims to unify the representation of proteoforms and peptidoforms. Therefore, this notation supports use cases needed for bottom-up and middle/topdown proteomics approaches and allows the encoding of highly modified proteins and peptides using a human and machine-readable string. ProForma 2.0 covers encoding protein modification names and accessions, cross-linking reagents including disulfides, glycans, modifications encoded using mass shifts and/or via chemical formulas, labile and C or N-terminal modifications, ambiguity in the modification position and representation of atomic isotopes, among other use cases. Notational conventions are based on public controlled vocabularies and ontologies. Detailed information about the notation and existing implementations are available at http://www.psidev.info/proforma and at the corresponding GitHub repository (https://github.com/HUPO-PSI/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}},
  keywords     = {{. ProForma,proteoform,peptidoform,top-down proteomics,file formats,data standards,mass spectrometry,FAIR}},
  language     = {{eng}},
  pages        = {{11}},
  series       = {{ARXIV}},
  title        = {{Proteomics standards initiatives ProForma 2.0 unifying the encoding of proteoforms and peptidoforms}},
  year         = {{2021}},
}