ProForma: A Standard Proteoform Notation

Richard D. Leduc*, Veit Schwämmle, Michael R. Shortreed, Anthony J. Cesnik, Stefan K. Solntsev, Jared B. Shaw, Maria J. Martin, Juan A. Vizcaino, Emanuele Alpi, Paul Danis, Neil L. Kelleher, Lloyd M. Smith, Ying Ge, Jeffrey N. Agar, Julia Chamot-Rooke, Joseph A. Loo, Ljiljana Pasa-Tolic, Yury O. Tsybin

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

17 Scopus citations

Abstract

The Consortium for Top-Down Proteomics (CTDP) proposes a standardized notation, ProForma, for writing the sequence of fully characterized proteoforms. ProForma provides a means to communicate any proteoform by writing the amino acid sequence using standard one-letter notation and specifying modifications or unidentified mass shifts within brackets following certain amino acids. The notation is unambiguous, human-readable, and can easily be parsed and written by bioinformatic tools. This system uses seven rules and supports a wide range of possible use cases, ensuring compatibility and reproducibility of proteoform annotations. Standardizing proteoform sequences will simplify storage, comparison, and reanalysis of proteomic studies, and the Consortium welcomes input and contributions from the research community on the continued design and maintenance of this standard.

Original languageEnglish (US)
Pages (from-to)1321-1325
Number of pages5
JournalJournal of Proteome Research
Volume17
Issue number3
DOIs
StatePublished - Mar 2 2018

Keywords

  • human readable
  • machine readable
  • proteoform
  • standard

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

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