IV. ProForma: a standardized notation for writing proteoform sequences

ProForma: a standardized notation for writing proteoform sequences

While the notation for writing protein sequences is defined by IUPAC, there is no such definition for proteoform sequences composed of both amino acids and PTMs at specific positions. These notations are important for communicating the results of protein and proteoform analyses, and so I worked with a subcommittee of the Consortium for Top-Down Proteomics (CTDP) to develop and define such a standard notation for writing proteoform sequences. I also contribute to a standard development kit in the C# computing language that implements this notation, including recent extensions for ambiguity in modification localizations.

Research Papers

(1) 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. “Proteomics Standards Initiative’s ProForma 2.0: Unifying the encoding of Proteoforms and Peptidoforms.” Journal of Proteome Research 2022, 21, 1189- 1195. PMC7612572.

(2) LeDuc, R.*; Schwämmle, V.*; Shortreed, M. R.*; Cesnik, A. J.*; Solntsev, S. K.*; Shaw, J.*; Martin, M. J.; Vizcaíno, J. A.; Alpi, E.; Danis, P.; Kelleher, N. L.; Smith, L. M.; Ge, Y.; Agar, J. N.; Chamot-Rooke, J.; Loo, J.; Paša-Tolić, L.; Tsybin, Y. O. “ProForma: a Standard Proteoform Notation.” Journal of Proteome Research 2018, 17, 1321–1325. PMC5837035. *Contributed equally