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

共 27 条

[1]

Apweiler R, 2004, NUCLEIC ACIDS RES, V32, pD115, DOI [10.1093/nar/gkw1099, 10.1093/nar/gkh131]

[2]

Armstrong D.R., 2020, NUCLEIC ACIDS RES, V48, pD335, DOI DOI 10.1093/NAR/GKZ990

[3] Proteomics Standards Initiative Extended FASTA Format [J].

Binz, Pierre-Alain ;

Shofstahl, Jim ;

Vizcaino, Juan Antonio ;

Barsnes, Harald ;

Chalkley, Robert J. ;

Menschaert, Gerben ;

Alpi, Emanuele ;

Clauser, Karl ;

Eng, Jimmy K. ;

Lane, Lydie ;

Seymour, Sean L. ;

Sanchez, Luis Francisco Hernandez ;

Mayer, Gerhard ;

Eisenacher, Martin ;

Perez-Riverol, Yasset ;

Kapp, Eugene A. ;

Mendoza, Luis ;

Baker, Peter R. ;

Collins, Andrew ;

Van den Bossche, Tim ;

Deutsch, Eric W. .

JOURNAL OF PROTEOME RESEARCH, 2019, 18 (06) :2686-2692

[4] spectrum_utils: A Python']Python Package for Mass Spectrometry Data Processing and Visualization [J].

Bittremieux, Wout .

ANALYTICAL CHEMISTRY, 2020, 92 (01) :659-661

[5] Unimod: Protein modifications for mass spectrometry [J].

Creasy, DM ;

Cottrell, JS .

PROTEOMICS, 2004, 4 (06) :1534-1536

[6] A proteomics sample metadata representation for multiomics integration and big data analysis [J].

Dai, Chengxin ;

Fullgrabe, Anja ;

Pfeuffer, Julianus ;

Solovyeva, Elizaveta M. ;

Deng, Jingwen ;

Moreno, Pablo ;

Kamatchinathan, Selvakumar ;

Kundu, Deepti Jaiswal ;

George, Nancy ;

Fexova, Silvie ;

Gruening, Bjoern ;

Foell, Melanie Christine ;

Griss, Johannes ;

Vaudel, Marc ;

Audain, Enrique ;

Locard-Paulet, Marie ;

Turewicz, Michael ;

Eisenacher, Martin ;

Uszkoreit, Julian ;

Van den Bossche, Tim ;

Schwammle, Veit ;

Webel, Henry ;

Schulze, Stefan ;

Bouyssie, David ;

Jayaram, Savita ;

Duggineni, Vinay Kumar ;

Samaras, Patroklos ;

Wilhelm, Mathias ;

Choi, Meena ;

Wang, Mingxun ;

Kohlbacher, Oliver ;

Brazma, Alvis ;

Papatheodorou, Irene ;

Bandeira, Nuno ;

Deutsch, Eric W. ;

Vizcaino, Juan Antonio ;

Bai, Mingze ;

Sachsenberg, Timo ;

Levitsky, Lev I. ;

Perez-Riverol, Yasset .

NATURE COMMUNICATIONS, 2021, 12 (01)

[7] Universal Spectrum Identifier for mass spectra [J].

Deutsch, Eric W. ;

Perez-Riverol, Yasset ;

Carver, Jeremy ;

Kawano, Shin ;

Mendoza, Luis ;

Van Den Bossche, Tim ;

Gabriels, Ralf ;

Binz, Pierre-Alain ;

Pullman, Benjamin ;

Sun, Zhi ;

Shofstahl, Jim ;

Bittremieux, Wout ;

Mak, Tytus D. ;

Klein, Joshua ;

Zhu, Yunping ;

Lam, Henry ;

Vizcaino, Juan Antonio ;

Bandeira, Nuno .

NATURE METHODS, 2021, 18 (07) :768-+

[8] The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics [J].

Deutsch, Eric W. ;

Bandeira, Nuno ;

Sharma, Vagisha ;

Perez-Riverol, Yasset ;

Carver, Jeremy J. ;

Kundu, Deepti J. ;

Garcia-Seisdedos, David ;

Jarnuczak, Andrew F. ;

Hewapathirana, Suresh ;

Pullman, Benjamin S. ;

Wertz, Julie ;

Sun, Zhi ;

Kawano, Shin ;

Okuda, Shujiro ;

Watanabe, Yu ;

Hermjakob, Henning ;

MacLean, Brendan ;

MacCoss, Michael J. ;

Zhu, Yunping ;

Ishihama, Yasushi ;

Vizcaino, Juan A. .

NUCLEIC ACIDS RESEARCH, 2020, 48 (D1) :D1145-D1152

[9] Development of data representation standards by the human proteome organization proteomics standards initiative [J].

Deutsch, Eric W. ;

Albar, Juan Pablo ;

Binz, Pierre-Alain ;

Eisenacher, Martin ;

Jones, Andrew R. ;

Mayer, Gerhard ;

Omenn, Gilbert S. ;

Orchard, Sandra ;

Vizcaino, Juan Antonio ;

Hermjakob, Henning .

JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION, 2015, 22 (03) :495-506

[10] The Reactome pathway Knowledgebase [J].

Fabregat, Antonio ;

Sidiropoulos, Konstantinos ;

Garapati, Phani ;

Gillespie, Marc ;

Hausmann, Kerstin ;

Haw, Robin ;

Jassal, Bijay ;

Jupe, Steven ;

Korninger, Florian ;

McKay, Sheldon ;

Matthews, Lisa ;

May, Bruce ;

Milacic, Marija ;

Rothfels, Karen ;

Shamovsky, Veronica ;

Webber, Marissa ;

Weiser, Joel ;

Williams, Mark ;

Wu, Guanming ;

Stein, Lincoln ;

Hermjakob, Henning ;

D'Eustachio, Peter .

NUCLEIC ACIDS RESEARCH, 2016, 44 (D1) :D481-D487

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