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Proteomics Standards Initiative : fifteen years of progress and future work

Eric W Deutsch, Sandra Orchard, Pierre-Alain Binz, Wout Bittremieux, Martin Eisenacher, Henning Hermjakob, Shin Kawano, Henry Lam, Gerhard Mayer, Gerben Menschaert (UGent) , et al.
(2017) JOURNAL OF PROTEOME RESEARCH. 16(12). p.4288-4298
Author
Organization
Abstract
The Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) has now been developing and promoting open community standards and software tools in the field of proteomics for 15 years. Under the guidance of the chair, cochairs, and other leadership positions, the PSI working groups are tasked with the development and maintenance of community standards via special workshops and ongoing work. Among the existing ratified standards, the PSI working groups continue to update PSI-MI XML, MITAB, mzML, mzIdentML, mzQuantML, mzTab, and the MIAPE (Minimum Information About a Proteomics Experiment) guidelines with the advance of new technologies and techniques. Furthermore, new standards are currently either in the final stages of completion (proBed and proBAM for proteogenomics results as well as PEFF) or in early stages of design (a spectral library standard format, a universal spectrum identifier, the qcML quality control format, and the Protein Expression Interface (PROXI) web services Application Programming Interface). In this work we review the current status of all of these aspects of the PSI, describe synergies with other efforts such as the ProteomeXchange Consortium, the Human Proteome Project, and the metabolomics community, and provide a look at future directions of the PSI.
Keywords
data standard, database, mass spectrometry, proteomics, metabolomics, protein identification, protein quantification, molecular interactions, bioinformatics software, quality control, MASS-SPECTROMETRY, GENOME BROWSER, DATABASE, ORGANIZATION, GUIDELINES, FORMAT, REPRESENTATION, CHROMATOGRAPHY, INFORMATICS, CONSORTIUM

Citation

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MLA
Deutsch, Eric W., et al. “Proteomics Standards Initiative : Fifteen Years of Progress and Future Work.” JOURNAL OF PROTEOME RESEARCH, vol. 16, no. 12, 2017, pp. 4288–98, doi:10.1021/acs.jproteome.7b00370.
APA
Deutsch, E. W., Orchard, S., Binz, P.-A., Bittremieux, W., Eisenacher, M., Hermjakob, H., … Jones, A. R. (2017). Proteomics Standards Initiative : fifteen years of progress and future work. https://doi.org/10.1021/acs.jproteome.7b00370
Chicago author-date
Deutsch, Eric W, Sandra Orchard, Pierre-Alain Binz, Wout Bittremieux, Martin Eisenacher, Henning Hermjakob, Shin Kawano, et al. 2017. “Proteomics Standards Initiative : Fifteen Years of Progress and Future Work.” JOURNAL OF PROTEOME RESEARCH. https://doi.org/10.1021/acs.jproteome.7b00370.
Chicago author-date (all authors)
Deutsch, Eric W, Sandra Orchard, Pierre-Alain Binz, Wout Bittremieux, Martin Eisenacher, Henning Hermjakob, Shin Kawano, Henry Lam, Gerhard Mayer, Gerben Menschaert, Yasset Perez-Riverol, Reza M Salek, David L Tabb, Stefan Tenzer, Juan Antonio Vizcaíno, Mathias Walzer, and Andrew R Jones. 2017. “Proteomics Standards Initiative : Fifteen Years of Progress and Future Work.” JOURNAL OF PROTEOME RESEARCH. doi:10.1021/acs.jproteome.7b00370.
Vancouver
1.
Deutsch EW, Orchard S, Binz P-A, Bittremieux W, Eisenacher M, Hermjakob H, et al. Proteomics Standards Initiative : fifteen years of progress and future work. Vol. 16, JOURNAL OF PROTEOME RESEARCH. 2017. p. 4288–98.
IEEE
[1]
E. W. Deutsch et al., “Proteomics Standards Initiative : fifteen years of progress and future work,” JOURNAL OF PROTEOME RESEARCH, vol. 16, no. 12. pp. 4288–4298, 2017.
@misc{8532023,
  abstract     = {{The Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) has now been developing and promoting open community standards and software tools in the field of proteomics for 15 years. Under the guidance of the chair, cochairs, and other leadership positions, the PSI working groups are tasked with the development and maintenance of community standards via special workshops and ongoing work. Among the existing ratified standards, the PSI working groups continue to update PSI-MI XML, MITAB, mzML, mzIdentML, mzQuantML, mzTab, and the MIAPE (Minimum Information About a Proteomics Experiment) guidelines with the advance of new technologies and techniques. Furthermore, new standards are currently either in the final stages of completion (proBed and proBAM for proteogenomics results as well as PEFF) or in early stages of design (a spectral library standard format, a universal spectrum identifier, the qcML quality control format, and the Protein Expression Interface (PROXI) web services Application Programming Interface). In this work we review the current status of all of these aspects of the PSI, describe synergies with other efforts such as the ProteomeXchange Consortium, the Human Proteome Project, and the metabolomics community, and provide a look at future directions of the PSI.}},
  author       = {{Deutsch, Eric W and Orchard, Sandra and Binz, Pierre-Alain and Bittremieux, Wout and Eisenacher, Martin and Hermjakob, Henning and Kawano, Shin and Lam, Henry and Mayer, Gerhard and Menschaert, Gerben and Perez-Riverol, Yasset and Salek, Reza M and Tabb, David L and Tenzer, Stefan and Vizcaíno, Juan Antonio and Walzer, Mathias and Jones, Andrew R}},
  issn         = {{1535-3893}},
  keywords     = {{data standard,database,mass spectrometry,proteomics,metabolomics,protein identification,protein quantification,molecular interactions,bioinformatics software,quality control,MASS-SPECTROMETRY,GENOME BROWSER,DATABASE,ORGANIZATION,GUIDELINES,FORMAT,REPRESENTATION,CHROMATOGRAPHY,INFORMATICS,CONSORTIUM}},
  language     = {{eng}},
  number       = {{12}},
  pages        = {{4288--4298}},
  series       = {{JOURNAL OF PROTEOME RESEARCH}},
  title        = {{Proteomics Standards Initiative : fifteen years of progress and future work}},
  url          = {{http://doi.org/10.1021/acs.jproteome.7b00370}},
  volume       = {{16}},
  year         = {{2017}},
}
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