Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms

被引：21

作者：

LeDuc, Richard D. ^{[3
]}

Deutsch, Eric W. ^{[1
]}

Binz, Pierre-Alain ^{[2
]}

Fellers, Ryan T. ^{[3
]}

Cesnik, Anthony J. ^{[4
,5
,6
]}

Klein, Joshua A. ^{[7
]}

Van den Bossche, Tim ^{[8
,9
]}

Gabriels, Ralf ^{[8
,9
]}

Yalavarthi, Arshika ^{[3
]}

Perez-Riverol, Yasset ^{[10
]}

Carver, Jeremy ^{[11
,12
]}

Bittremieux, Wout ^{[12
,13
]}

Kawano, Shin ^{[14
,15
]}

Pullman, Benjamin ^{[13
,16
]}

Bandeira, Nuno ^{[11
,12
]}

Kelleher, Neil L. ^{[3
]}

Thomas, Paul M. ^{[3
,17
]}

Vizcaino, Juan Antonio ^{[10
]}

机构：

[1] Inst Syst Biol, Seattle, WA 98109 USA

[2] Lausanne Univ Hosp, Clin Chem Serv, CH-1011 Lausanne, Switzerland

[3] Northwestern Univ, Natl Resource Translat & Dev Prote, Evanston, IL 60611 USA

[4] Stanford Univ, Dept Genet, Stanford, CA 94305 USA

[5] Chan Zuckerberg Biohub, San Francisco, CA 94158 USA

[6] KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, SciLifeLab, S-11351 Stockholm, Sweden

[7] Boston Univ, Program Bioinformat, Boston, MA 02215 USA

[8] VIB UGent Ctr Med Biotechnol, B-9052 Ghent, Belgium

[9] Univ Ghent, Fac Med & Hlth Sci, Dept Biomol Med, B-9000 Ghent, Belgium

[10] EMBL European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Cambridge CB10 1SD, England

[11] UCSD, Ctr Computat Mass Spectrometry, Dept Comp Sci & Engn, La Jolla, CA 92093 USA

[12] UCSD, Skaggs Sch Pharm & Pharmaceut Sci, La Jolla, CA 92093 USA

[13] UCSD, Ctr Computat Mass Spectrometry, La Jolla, CA 92093 USA

[14] Toyama Univ Int Studies, Toyama, Toyama 9301292, Japan

[15] Res Org Informat & Syst, Joint Support Ctr Data Sci Res, Database Ctr Life Sci, Kashiwa, Chiba 2770871, Japan

[16] UCSD, Dept Comp Sci & Engn, La Jolla, CA 92093 USA

[17] AbbVie Inc, 1401 Sheridan Rd, N Chicago, IL 60064 USA

来源：

JOURNAL OF PROTEOME RESEARCH | 2022年 / 21卷 / 04期

基金：

美国国家科学基金会; 日本科学技术振兴机构; 美国国家卫生研究院; 英国生物技术与生命科学研究理事会; 瑞典研究理事会; 日本学术振兴会;

关键词：

ProForma; proteoform; peptidoform; top-down proteomics; file formats; data standards; mass spectrometry; FAIR; PROTEIN MODIFICATIONS; PROTEOMICS; REPRESENTATION; RESOURCE; DATABASE;

D O I：

10.1021/acs.jproteome.1c00771

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

It is important for the proteomics community to have a standardizedmanner to represent all possible variations of a protein or peptide primary sequence,including natural, chemically induced, and artifactual modifications. The HumanProteome Organization Proteomics Standards Initiative in collaboration with severalmembers of the Consortium for Top-Down Proteomics (CTDP) has developed astandard notation called ProForma 2.0, which is a substantial extension of the originalProForma notation developed by the CTDP. ProForma 2.0 aims to unify therepresentation of proteoforms and peptidoforms. ProForma 2.0 supports use casesneeded for bottom-up and middle-/top-down proteomics approaches and allows theencoding of highly modified proteins and peptides using a human- and machine-readable string. ProForma 2.0 can be used to represent protein modifications in a specified or ambiguous location, designated bymass shifts, chemical formulas, or controlled vocabulary terms, including cross-links (natural and chemical) and atomic isotopes.Notational conventions are based on public controlled vocabularies and ontologies. The most up-to-date full specification documentand information about software implementations are available athttp://psidev.info/proforma.

引用

页码：1189 / 1195

页数：7

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