ProForma: A Standard Proteoform Notation

被引：36

作者：

LeDuc, Richard D. ^{[1
]}

Schwammle, Veit ^{[2
]}

Shortreed, Michael R. ^{[3
]}

Cesnik, Anthony J. ^{[3
]}

Solntsev, Stefan K. ^{[3
]}

Shaw, Jared B. ^{[4
]}

Martin, Maria J. ^{[5
]}

Vizcaino, Juan A. ^{[5
]}

Alpi, Emanuele ^{[5
,8
]}

Danis, Paul ^{[6
]}

Kelleher, Neil L. ^{[1
]}

Smith, Lloyd M. ^{[3
,7
]}

Ge, Ying ^{[3
]}

Agar, Jeffrey N. ^{[8
]}

Chamot-Rooke, Julia ^{[9
]}

Loo, Joseph A.

Pasa-Tolic, Ljiljana ^{[4
]}

Tsybin, Yury O. ^{[8
,10
]}

机构：

[1] Northwestern Univ, Natl Resource Translat & Dev Prote, Evanston, IL 60208 USA

[2] Univ Southern Denmark, Dept Biochem & Mol Biol, DK-5230 Odense, Denmark

[3] Univ Wisconsin, Dept Chem, 1101 Univ Ave, Madison, WI 53706 USA

[4] Pacific Northwest Natl Lab, Environm Mol Sci Lab, Richland, WA 99354 USA

[5] European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England

[6] Consortium Top Down Prote, Cambridge, MA 02142 USA

[7] Univ Wisconsin, Genome Ctr Wisconsin, Madison, WI 53706 USA

[8] Northeastern Univ, Chem & Chem Biol, Boston, MA 02115 USA

[9] Inst Pasteur, CNRS, USR 2000, Mass Spectrometry Biol Unit, Paris 15, France

[10] Spectroswiss, CH-1015 Lausanne, Switzerland

来源：

JOURNAL OF PROTEOME RESEARCH | 2018年 / 17卷 / 03期

关键词：

standard; proteoform; human readable; machine readable; PROTEIN MODIFICATIONS; MASS; REPRESENTATION; DATABASE;

D O I：

10.1021/acs.jproteome.7b00851

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：1321 / 1325

页数：5

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