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

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Resumé

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.

OriginalsprogEngelsk
TidsskriftJournal of Proteome Research
Vol/bind17
Udgave nummer3
Sider (fra-til)1321-1325
ISSN1535-3893
DOI
StatusUdgivet - 2018

Fingeraftryk

Amino Acids
Bioinformatics
Computational Biology
Maintenance
Research
Proteomics

Citer dette

LeDuc, R. D., Schwämmle, V., Shortreed, M. R., Cesnik, A. J., Solntsev, S. K., Shaw, J. B., ... Tsybin, Y. O. (2018). ProForma: A Standard Proteoform Notation. Journal of Proteome Research, 17(3), 1321-1325. https://doi.org/10.1021/acs.jproteome.7b00851
LeDuc, Richard D ; Schwämmle, Veit ; Shortreed, Michael R ; Cesnik, Anthony J ; Solntsev, Stefan K ; Shaw, Jared B ; Martin, Maria J ; Vizcaino, Juan A ; Alpi, Emanuele ; Danis, Paul ; Kelleher, Neil L ; Smith, Lloyd M ; Ge, Ying ; Agar, Jeffrey N ; Chamot-Rooke, Julia ; Loo, Joseph A ; Pasa-Tolic, Ljiljana ; Tsybin, Yury O. / ProForma : A Standard Proteoform Notation. I: Journal of Proteome Research. 2018 ; Bind 17, Nr. 3. s. 1321-1325.
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title = "ProForma: A Standard Proteoform Notation",
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.",
author = "LeDuc, {Richard D} and Veit Schw{\"a}mmle and Shortreed, {Michael R} and Cesnik, {Anthony J} and Solntsev, {Stefan K} and Shaw, {Jared B} and Martin, {Maria J} and Vizcaino, {Juan A} and Emanuele Alpi and Paul Danis and Kelleher, {Neil L} and Smith, {Lloyd M} and Ying Ge and Agar, {Jeffrey N} and Julia Chamot-Rooke and Loo, {Joseph A} and Ljiljana Pasa-Tolic and Tsybin, {Yury O}",
year = "2018",
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LeDuc, RD, Schwämmle, V, Shortreed, MR, Cesnik, AJ, Solntsev, SK, Shaw, JB, Martin, MJ, Vizcaino, JA, Alpi, E, Danis, P, Kelleher, NL, Smith, LM, Ge, Y, Agar, JN, Chamot-Rooke, J, Loo, JA, Pasa-Tolic, L & Tsybin, YO 2018, 'ProForma: A Standard Proteoform Notation', Journal of Proteome Research, bind 17, nr. 3, s. 1321-1325. https://doi.org/10.1021/acs.jproteome.7b00851

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

I: Journal of Proteome Research, Bind 17, Nr. 3, 2018, s. 1321-1325.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - ProForma

T2 - A Standard Proteoform Notation

AU - LeDuc, Richard D

AU - Schwämmle, Veit

AU - Shortreed, Michael R

AU - Cesnik, Anthony J

AU - Solntsev, Stefan K

AU - Shaw, Jared B

AU - Martin, Maria J

AU - Vizcaino, Juan A

AU - Alpi, Emanuele

AU - Danis, Paul

AU - Kelleher, Neil L

AU - Smith, Lloyd M

AU - Ge, Ying

AU - Agar, Jeffrey N

AU - Chamot-Rooke, Julia

AU - Loo, Joseph A

AU - Pasa-Tolic, Ljiljana

AU - Tsybin, Yury O

PY - 2018

Y1 - 2018

N2 - 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.

AB - 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.

U2 - 10.1021/acs.jproteome.7b00851

DO - 10.1021/acs.jproteome.7b00851

M3 - Journal article

VL - 17

SP - 1321

EP - 1325

JO - Journal of Proteome Research

JF - Journal of Proteome Research

SN - 1535-3893

IS - 3

ER -

LeDuc RD, Schwämmle V, Shortreed MR, Cesnik AJ, Solntsev SK, Shaw JB et al. ProForma: A Standard Proteoform Notation. Journal of Proteome Research. 2018;17(3):1321-1325. https://doi.org/10.1021/acs.jproteome.7b00851