publication . Review . Article . Other literature type . 2017

Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.

Sandra Orchard; Eric W. Deutsch; Wout Bittremieux; Mathias Walzer; Reza M. Salek; Yasset Perez-Riverol; Andrew R. Jones; Martin Eisenacher; Shin Kawano; Henry H N Lam; ...
Open Access English
  • Published: 01 Dec 2017
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 t...
Subjects
free text keywords: bioinformatics software; data standard; database; mass spectrometry; metabolomics; molecular interactions; protein identification; protein quantification; proteomics; quality control, Perspective, data standard, database, mass spectrometry, proteomics, metabolomics, protein identification, protein quantification, molecular interactions, bioinformatics software, quality control, Emerging technologies, Human proteome project, Application programming interface, Proteomics Standards Initiative, XML, computer.internet_protocol, computer, Data science, Working group, Web service, computer.software_genre, Community standards, Computer science
Funded by
WT
Project
  • Funder: Wellcome Trust (WT)
,
RCUK| ProteoGenomics: Dynamic Linkage of Genomes and Proteomes through Ensembl and ProteomeXchange
Project
  • Funder: Research Council UK (RCUK)
  • Project Code: BB/L024128/1
  • Funding stream: BBSRC
,
NIH| Development of Trans Proteomic Pipeline, an Analysis Suite for Mass Spectrometry
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM087221-07
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
NIH| Advancing data and metadata standards for proteomics mass spectra
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1R24GM127667-01
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
RCUK| MIDAS - Molecular Interaction Data Availability Standards
Project
  • Funder: Research Council UK (RCUK)
  • Project Code: BB/L024179/1
  • Funding stream: BBSRC
63 references, page 1 of 5

Deutsch E. W.File formats commonly used in mass spectrometry proteomics. Mol. Cell. Proteomics 2012, 11 (12), 1612–1621. 10.1074/mcp.R112.019695.22956731 [OpenAIRE] [PubMed] [DOI]

Hanash S.; Celis J. E.The Human Proteome Organization: a mission to advance proteome knowle dge. Mol. Cell. Proteomics 2002, 1 (6), 413–414. 10.1074/mcp.R200002-MCP200.12169681 [PubMed] [DOI]

Orchard S.; Hermjakob H.; Apweiler R.The proteomics standards initiative. Proteomics 2003, 3 (7), 1374–1376. 10.1002/pmic.200300496.12872238 [OpenAIRE] [PubMed] [DOI]

Deutsch E. W.; Albar J. P.; Binz P.-A.; Eisenacher M.; Jones A. R.; Mayer G.; Omenn G. S.; Orchard S.; Vizcaíno J. A.; Hermjakob H.Development of data representation standards by the human proteome organization proteomics standards initiative. J. Am. Med. Inform. Assoc. JAMIA 2015, 22 (3), 495–506. 10.1093/jamia/ocv001.25726569 [OpenAIRE] [PubMed] [DOI]

Mayer G.; Jones A. R.; Binz P.-A.; Deutsch E. W.; Orchard S.; Montecchi-Palazzi L.; Vizcaíno J. A.; Hermjakob H.; Oveillero D.; Julian R.; et al. Controlled vocabularies and ontologies in proteomics: overview, principles and practice. Biochim. Biophys. Acta, Proteins Proteomics 2014, 1844 (1 Pt A), 98–107. 10.1016/j.bbapap.2013.02.017. [OpenAIRE] [DOI]

Vizcaíno J. A.; Martens L.; Hermjakob H.; Julian R. K.; Paton N. W.The PSI formal document process and its implementation on the PSI website. Proteomics 2007, 7 (14), 2355–2357. 10.1002/pmic.200700064.17570517 [OpenAIRE] [PubMed] [DOI]

Walzer M.; Pernas L. E.; Nasso S.; Bittremieux W.; Nahnsen S.; Kelchtermans P.; Pichler P.; van den Toorn H. W. P.; Staes A.; Vandenbussche J.; et al. qcML: an exchange format for quality control metrics from mass spectrometry experiments. Mol. Cell. Proteomics 2014, 13 (8), 1905–1913. 10.1074/mcp.M113.035907.24760958 [OpenAIRE] [PubMed] [DOI]

Feng J.; Ding C.; Qiu N.; Ni X.; Zhan D.; Liu W.; Xia X.; Li P.; Lu B.; Zhao Q.; et al. Firmiana: towards a one-stop proteomic cloud platform for data processing and analysis. Nat. Biotechnol.2017, 35 (5), 409–412. 10.1038/nbt.3825.28486446 [OpenAIRE] [PubMed] [DOI]

Kerrien S.; Orchard S.; Montecchi-Palazzi L.; Aranda B.; Quinn A. F.; Vinod N.; Bader G. D.; Xenarios I.; Wojcik J.; Sherman D.; et al. Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol.2007, 5, 44 10.1186/1741-7007-5-44.17925023 [OpenAIRE] [PubMed] [DOI]

Orchard S.; Kerrien S.; Abbani S.; Aranda B.; Bhate J.; Bidwell S.; Bridge A.; Briganti L.; Brinkman F. S. L.; Brinkman F.; et al. Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat. Methods 2012, 9 (4), 345–350. 10.1038/nmeth.1931.22453911 [OpenAIRE] [PubMed] [DOI]

Aranda B.; Blankenburg H.; Kerrien S.; Brinkman F. S. L.; Ceol A.; Chautard E.; Dana J. M.; De Las Rivas J.; Dumousseau M.; Galeota E.; et al. PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat. Methods 2011, 8 (7), 528–529. 10.1038/nmeth.1637.21716279 [OpenAIRE] [PubMed] [DOI]

Martens L.; Chambers M.; Sturm M.; Kessner D.; Levander F.; Shofstahl J.; Tang W. H.; Römpp A.; Neumann S.; Pizarro A. D.; et al. mzML--a community standard for mass spectrometry data. Mol. Cell. Proteomics 2011, 10 (1), R110.000133 10.1074/mcp.R110.000133. [DOI]

Deutsch E. W.Mass spectrometer output file format mzML. Methods Mol. Biol.2010, 604, 319–331. 10.1007/978-1-60761-444-9_22.20013381 [OpenAIRE] [PubMed] [DOI]

Teleman J.; Dowsey A. W.; Gonzalez-Galarza F. F.; Perkins S.; Pratt B.; Röst H. L.; Malmström L.; Malmström J.; Jones A. R.; Deutsch E. W.; et al. Numerical compression schemes for proteomics mass spectrometry data. Mol. Cell. Proteomics 2014, 13 (6), 1537–1542. 10.1074/mcp.O114.037879.24677029 [OpenAIRE] [PubMed] [DOI]

Jones A. R.; Eisenacher M.; Mayer G.; Kohlbacher O.; Siepen J.; Hubbard S. J.; Selley J. N.; Searle B. C.; Shofstahl J.; Seymour S. L.; et al. The mzIdentML data standard for mass spectrometry-based proteomics results. Mol. Cell. Proteomics 2012, 11 (7), M111.014381 10.1074/mcp.M111.014381. [DOI]

63 references, page 1 of 5
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 t...
Subjects
free text keywords: bioinformatics software; data standard; database; mass spectrometry; metabolomics; molecular interactions; protein identification; protein quantification; proteomics; quality control, Perspective, data standard, database, mass spectrometry, proteomics, metabolomics, protein identification, protein quantification, molecular interactions, bioinformatics software, quality control, Emerging technologies, Human proteome project, Application programming interface, Proteomics Standards Initiative, XML, computer.internet_protocol, computer, Data science, Working group, Web service, computer.software_genre, Community standards, Computer science
Funded by
WT
Project
  • Funder: Wellcome Trust (WT)
,
RCUK| ProteoGenomics: Dynamic Linkage of Genomes and Proteomes through Ensembl and ProteomeXchange
Project
  • Funder: Research Council UK (RCUK)
  • Project Code: BB/L024128/1
  • Funding stream: BBSRC
,
NIH| Development of Trans Proteomic Pipeline, an Analysis Suite for Mass Spectrometry
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM087221-07
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
NIH| Advancing data and metadata standards for proteomics mass spectra
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1R24GM127667-01
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
RCUK| MIDAS - Molecular Interaction Data Availability Standards
Project
  • Funder: Research Council UK (RCUK)
  • Project Code: BB/L024179/1
  • Funding stream: BBSRC
63 references, page 1 of 5

Deutsch E. W.File formats commonly used in mass spectrometry proteomics. Mol. Cell. Proteomics 2012, 11 (12), 1612–1621. 10.1074/mcp.R112.019695.22956731 [OpenAIRE] [PubMed] [DOI]

Hanash S.; Celis J. E.The Human Proteome Organization: a mission to advance proteome knowle dge. Mol. Cell. Proteomics 2002, 1 (6), 413–414. 10.1074/mcp.R200002-MCP200.12169681 [PubMed] [DOI]

Orchard S.; Hermjakob H.; Apweiler R.The proteomics standards initiative. Proteomics 2003, 3 (7), 1374–1376. 10.1002/pmic.200300496.12872238 [OpenAIRE] [PubMed] [DOI]

Deutsch E. W.; Albar J. P.; Binz P.-A.; Eisenacher M.; Jones A. R.; Mayer G.; Omenn G. S.; Orchard S.; Vizcaíno J. A.; Hermjakob H.Development of data representation standards by the human proteome organization proteomics standards initiative. J. Am. Med. Inform. Assoc. JAMIA 2015, 22 (3), 495–506. 10.1093/jamia/ocv001.25726569 [OpenAIRE] [PubMed] [DOI]

Mayer G.; Jones A. R.; Binz P.-A.; Deutsch E. W.; Orchard S.; Montecchi-Palazzi L.; Vizcaíno J. A.; Hermjakob H.; Oveillero D.; Julian R.; et al. Controlled vocabularies and ontologies in proteomics: overview, principles and practice. Biochim. Biophys. Acta, Proteins Proteomics 2014, 1844 (1 Pt A), 98–107. 10.1016/j.bbapap.2013.02.017. [OpenAIRE] [DOI]

Vizcaíno J. A.; Martens L.; Hermjakob H.; Julian R. K.; Paton N. W.The PSI formal document process and its implementation on the PSI website. Proteomics 2007, 7 (14), 2355–2357. 10.1002/pmic.200700064.17570517 [OpenAIRE] [PubMed] [DOI]

Walzer M.; Pernas L. E.; Nasso S.; Bittremieux W.; Nahnsen S.; Kelchtermans P.; Pichler P.; van den Toorn H. W. P.; Staes A.; Vandenbussche J.; et al. qcML: an exchange format for quality control metrics from mass spectrometry experiments. Mol. Cell. Proteomics 2014, 13 (8), 1905–1913. 10.1074/mcp.M113.035907.24760958 [OpenAIRE] [PubMed] [DOI]

Feng J.; Ding C.; Qiu N.; Ni X.; Zhan D.; Liu W.; Xia X.; Li P.; Lu B.; Zhao Q.; et al. Firmiana: towards a one-stop proteomic cloud platform for data processing and analysis. Nat. Biotechnol.2017, 35 (5), 409–412. 10.1038/nbt.3825.28486446 [OpenAIRE] [PubMed] [DOI]

Kerrien S.; Orchard S.; Montecchi-Palazzi L.; Aranda B.; Quinn A. F.; Vinod N.; Bader G. D.; Xenarios I.; Wojcik J.; Sherman D.; et al. Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol.2007, 5, 44 10.1186/1741-7007-5-44.17925023 [OpenAIRE] [PubMed] [DOI]

Orchard S.; Kerrien S.; Abbani S.; Aranda B.; Bhate J.; Bidwell S.; Bridge A.; Briganti L.; Brinkman F. S. L.; Brinkman F.; et al. Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat. Methods 2012, 9 (4), 345–350. 10.1038/nmeth.1931.22453911 [OpenAIRE] [PubMed] [DOI]

Aranda B.; Blankenburg H.; Kerrien S.; Brinkman F. S. L.; Ceol A.; Chautard E.; Dana J. M.; De Las Rivas J.; Dumousseau M.; Galeota E.; et al. PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat. Methods 2011, 8 (7), 528–529. 10.1038/nmeth.1637.21716279 [OpenAIRE] [PubMed] [DOI]

Martens L.; Chambers M.; Sturm M.; Kessner D.; Levander F.; Shofstahl J.; Tang W. H.; Römpp A.; Neumann S.; Pizarro A. D.; et al. mzML--a community standard for mass spectrometry data. Mol. Cell. Proteomics 2011, 10 (1), R110.000133 10.1074/mcp.R110.000133. [DOI]

Deutsch E. W.Mass spectrometer output file format mzML. Methods Mol. Biol.2010, 604, 319–331. 10.1007/978-1-60761-444-9_22.20013381 [OpenAIRE] [PubMed] [DOI]

Teleman J.; Dowsey A. W.; Gonzalez-Galarza F. F.; Perkins S.; Pratt B.; Röst H. L.; Malmström L.; Malmström J.; Jones A. R.; Deutsch E. W.; et al. Numerical compression schemes for proteomics mass spectrometry data. Mol. Cell. Proteomics 2014, 13 (6), 1537–1542. 10.1074/mcp.O114.037879.24677029 [OpenAIRE] [PubMed] [DOI]

Jones A. R.; Eisenacher M.; Mayer G.; Kohlbacher O.; Siepen J.; Hubbard S. J.; Selley J. N.; Searle B. C.; Shofstahl J.; Seymour S. L.; et al. The mzIdentML data standard for mass spectrometry-based proteomics results. Mol. Cell. Proteomics 2012, 11 (7), M111.014381 10.1074/mcp.M111.014381. [DOI]

63 references, page 1 of 5
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