Open Access

Nucleic Acids Research, volume 44, issue D1, pages D447-D456

2016 update of the PRIDE database and its related tools

Vizcaíno Juan Antonio ^{1, 2, 3}

Csordas Attila ^{1, 2, 3}

Del Toro Noemi ^{1, 2, 3}

Dianes José A ^{1, 2, 3}

Griss Johannes

Lavidas Ilias ^{1, 2, 3}

Mayer Gerhard ⁴

Perez-Riverol Yasset ^{1, 2, 3}

Reisinger Florian ^{1, 2, 3}

Ternent Tobias ^{1, 2, 3}

Xu Qing Wei ⁵

Wang Rui ^{1, 2, 3}

Hermjakob Henning ⁶

Hide authors affiliations Show authors affiliations: 6 affiliations

European Bioinformatics Institute (EMBL-EBI) |

Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK |

EUROPEAN MOLECULAR BIOLOGY LABORATORY

⁴

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany. |

⁵

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK Department of Computer Science and Technology, Hubei University of Education, Wuhan, China. |

⁶

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK National Center for Protein Sciences, Beijing, China. |

Publication type: Journal Article

Publication date: 2015-11-02

Oxford University Press

Journal: Nucleic Acids Research

Quartile SCImago

Quartile WOS

Impact factor: 14.9

ISSN: 03051048, 13624962

DOI: 10.1093/nar/gkv1145

Copy DOI

PubMed ID: 26527722

Genetics

Abstract

The PRoteomics IDEntifications (PRIDE) database is one of the world-leading data repositories of mass spectrometry (MS)-based proteomics data. Since the beginning of 2014, PRIDE Archive (http://www.ebi.ac.uk/pride/archive/) is the new PRIDE archival system, replacing the original PRIDE database. Here we summarize the developments in PRIDE resources and related tools since the previous update manuscript in the Database Issue in 2013. PRIDE Archive constitutes a complete redevelopment of the original PRIDE, comprising a new storage backend, data submission system and web interface, among other components. PRIDE Archive supports the most-widely used PSI (Proteomics Standards Initiative) data standard formats (mzML and mzIdentML) and implements the data requirements and guidelines of the ProteomeXchange Consortium. The wide adoption of ProteomeXchange within the community has triggered an unprecedented increase in the number of submitted data sets (around 150 data sets per month). We outline some statistics on the current PRIDE Archive data contents. We also report on the status of the PRIDE related stand-alone tools: PRIDE Inspector, PRIDE Converter 2 and the ProteomeXchange submission tool. Finally, we will give a brief update on the resources under development 'PRIDE Cluster' and 'PRIDE Proteomes', which provide a complementary view and quality-scored information of the peptide and protein identification data available in PRIDE Archive.

By date By citations

Citations by journals

	20 40 60 80 100 120 140 160 180 200
Journal of Proteome Research	Journal of Proteome Research, 183, 6.83% Journal of Proteome Research 183 publications, 6.83%
Molecular and Cellular Proteomics	Molecular and Cellular Proteomics, 154, 5.74% Molecular and Cellular Proteomics 154 publications, 5.74%
Scientific Reports	Scientific Reports, 111, 4.14% Scientific Reports 111 publications, 4.14%
Nature Communications	Nature Communications, 109, 4.07% Nature Communications 109 publications, 4.07%
Journal of Proteomics	Journal of Proteomics, 103, 3.84% Journal of Proteomics 103 publications, 3.84%
Proteomics	Proteomics, 60, 2.24% Proteomics 60 publications, 2.24%
PLoS ONE	PLoS ONE, 56, 2.09% PLoS ONE 56 publications, 2.09%
Frontiers in Microbiology	Frontiers in Microbiology, 51, 1.9% Frontiers in Microbiology 51 publications, 1.9%
Nucleic Acids Research	Nucleic Acids Research, 38, 1.42% Nucleic Acids Research 38 publications, 1.42%
Frontiers in Plant Science	Frontiers in Plant Science, 38, 1.42% Frontiers in Plant Science 38 publications, 1.42%
International Journal of Molecular Sciences	International Journal of Molecular Sciences, 37, 1.38% International Journal of Molecular Sciences 37 publications, 1.38%
Journal of Biological Chemistry	Journal of Biological Chemistry, 34, 1.27% Journal of Biological Chemistry 34 publications, 1.27%
Analytical Chemistry	Analytical Chemistry, 33, 1.23% Analytical Chemistry 33 publications, 1.23%
Cell Reports	Cell Reports, 29, 1.08% Cell Reports 29 publications, 1.08%
Proceedings of the National Academy of Sciences of the United States of America	Proceedings of the National Academy of Sciences of the United States of America, 27, 1.01% Proceedings of the National Academy of Sciences of the United States of America 27 publications, 1.01%
Data in Brief	Data in Brief, 25, 0.93% Data in Brief 25 publications, 0.93%
Frontiers in Immunology	Frontiers in Immunology, 20, 0.75% Frontiers in Immunology 20 publications, 0.75%
eLife	eLife, 20, 0.75% eLife 20 publications, 0.75%
Nature	Nature, 19, 0.71% Nature 19 publications, 0.71%
EMBO Reports	EMBO Reports, 18, 0.67% EMBO Reports 18 publications, 0.67%
Proteomics - Clinical Applications	Proteomics - Clinical Applications, 18, 0.67% Proteomics - Clinical Applications 18 publications, 0.67%
Environmental Microbiology	Environmental Microbiology, 17, 0.63% Environmental Microbiology 17 publications, 0.63%
mBio	mBio, 17, 0.63% mBio 17 publications, 0.63%
Cell	Cell, 15, 0.56% Cell 15 publications, 0.56%
BMC Genomics	BMC Genomics, 14, 0.52% BMC Genomics 14 publications, 0.52%
Communications Biology	Communications Biology, 13, 0.48% Communications Biology 13 publications, 0.48%
Clinical Proteomics	Clinical Proteomics, 13, 0.48% Clinical Proteomics 13 publications, 0.48%
Scientific data	Scientific data, 13, 0.48% Scientific data 13 publications, 0.48%
Electrophoresis	Electrophoresis, 13, 0.48% Electrophoresis 13 publications, 0.48%
	20 40 60 80 100 120 140 160 180 200

Citations by publishers

	100 200 300 400 500 600
Springer Nature	Springer Nature, 513, 19.13% Springer Nature 513 publications, 19.13%
Elsevier	Elsevier, 417, 15.55% Elsevier 417 publications, 15.55%
American Chemical Society (ACS)	American Chemical Society (ACS), 252, 9.4% American Chemical Society (ACS) 252 publications, 9.4%
Wiley	Wiley, 233, 8.69% Wiley 233 publications, 8.69%
American Society for Biochemistry and Molecular Biology	American Society for Biochemistry and Molecular Biology, 188, 7.01% American Society for Biochemistry and Molecular Biology 188 publications, 7.01%
Frontiers Media S.A.	Frontiers Media S.A., 141, 5.26% Frontiers Media S.A. 141 publications, 5.26%
Oxford University Press	Oxford University Press, 106, 3.95% Oxford University Press 106 publications, 3.95%
Multidisciplinary Digital Publishing Institute (MDPI)	Multidisciplinary Digital Publishing Institute (MDPI), 98, 3.66% Multidisciplinary Digital Publishing Institute (MDPI) 98 publications, 3.66%
Public Library of Science (PLoS)	Public Library of Science (PLoS), 80, 2.98% Public Library of Science (PLoS) 80 publications, 2.98%
American Society for Microbiology	American Society for Microbiology, 67, 2.5% American Society for Microbiology 67 publications, 2.5%
EMBO press	EMBO press, 32, 1.19% EMBO press 32 publications, 1.19%
Proceedings of the National Academy of Sciences (PNAS)	Proceedings of the National Academy of Sciences (PNAS), 27, 1.01% Proceedings of the National Academy of Sciences (PNAS) 27 publications, 1.01%
Taylor & Francis	Taylor & Francis, 23, 0.86% Taylor & Francis 23 publications, 0.86%
American Association for the Advancement of Science (AAAS)	American Association for the Advancement of Science (AAAS), 23, 0.86% American Association for the Advancement of Science (AAAS) 23 publications, 0.86%
eLife Sciences Publications	eLife Sciences Publications, 20, 0.75% eLife Sciences Publications 20 publications, 0.75%
Royal Society of Chemistry (RSC)	Royal Society of Chemistry (RSC), 14, 0.52% Royal Society of Chemistry (RSC) 14 publications, 0.52%
Impact Journals	Impact Journals, 12, 0.45% Impact Journals 12 publications, 0.45%
PeerJ	PeerJ, 12, 0.45% PeerJ 12 publications, 0.45%
Rockefeller University Press	Rockefeller University Press, 12, 0.45% Rockefeller University Press 12 publications, 0.45%
Cold Spring Harbor Laboratory	Cold Spring Harbor Laboratory, 12, 0.45% Cold Spring Harbor Laboratory 12 publications, 0.45%
The Company of Biologists	The Company of Biologists, 10, 0.37% The Company of Biologists 10 publications, 0.37%
Mary Ann Liebert	Mary Ann Liebert, 9, 0.34% Mary Ann Liebert 9 publications, 0.34%
American Society of Nephrology	American Society of Nephrology, 8, 0.3% American Society of Nephrology 8 publications, 0.3%
American Physiological Society	American Physiological Society, 8, 0.3% American Physiological Society 8 publications, 0.3%
American Society of Hematology	American Society of Hematology, 6, 0.22% American Society of Hematology 6 publications, 0.22%
SAGE	SAGE, 5, 0.19% SAGE 5 publications, 0.19%
Federation of American Societies for Experimental Biology (FASEB)	Federation of American Societies for Experimental Biology (FASEB), 5, 0.19% Federation of American Societies for Experimental Biology (FASEB) 5 publications, 0.19%
IOS Press	IOS Press, 4, 0.15% IOS Press 4 publications, 0.15%
Social Science Electronic Publishing	Social Science Electronic Publishing, 4, 0.15% Social Science Electronic Publishing 4 publications, 0.15%
	100 200 300 400 500 600

We do not take into account publications that without a DOI.
Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
Statistics recalculated weekly.

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Vizcaíno J. A. et al. 2016 update of the PRIDE database and its related tools // Nucleic Acids Research. 2015. Vol. 44. No. D1. p. D447-D456.

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Vizcaíno J. A., Csordas A., Del Toro N., Dianes J. A., Griss J., Lavidas I., Mayer G., Perez-Riverol Y., Reisinger F., Ternent T., Xu Q. W., Wang R., Hermjakob H. 2016 update of the PRIDE database and its related tools // Nucleic Acids Research. 2015. Vol. 44. No. D1. p. D447-D456.

RIS |

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RIS Copy

TY - JOUR

DO - 10.1093/nar/gkv1145

UR - https://doi.org/10.1093%2Fnar%2Fgkv1145

TI - 2016 update of the PRIDE database and its related tools

T2 - Nucleic Acids Research

AU - Vizcaíno, Juan Antonio

AU - Csordas, Attila

AU - Del Toro, Noemi

AU - Dianes, José A

AU - Griss, Johannes

AU - Lavidas, Ilias

AU - Mayer, Gerhard

AU - Perez-Riverol, Yasset

AU - Reisinger, Florian

AU - Ternent, Tobias

AU - Xu, Qing Wei

AU - Wang, Rui

AU - Hermjakob, Henning

PY - 2015

DA - 2015/11/02 00:00:00

PB - Oxford University Press

SP - D447-D456

IS - D1

VL - 44

PMID - 26527722

SN - 0305-1048

SN - 1362-4962

ER -

BibTex |

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@article{2015_Vizcaíno,

author = {Juan Antonio Vizcaíno and Attila Csordas and Noemi Del Toro and José A Dianes and Johannes Griss and Ilias Lavidas and Gerhard Mayer and Yasset Perez-Riverol and Florian Reisinger and Tobias Ternent and Qing Wei Xu and Rui Wang and Henning Hermjakob},

title = {2016 update of the PRIDE database and its related tools},

journal = {Nucleic Acids Research},

year = {2015},

volume = {44},

publisher = {Oxford University Press},

month = {nov},

url = {https://doi.org/10.1093%2Fnar%2Fgkv1145},

number = {D1},

pages = {D447--D456},

doi = {10.1093/nar/gkv1145}

}

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Vizcaíno, Juan Antonio, et al. “2016 update of the PRIDE database and its related tools.” Nucleic Acids Research, vol. 44, no. D1, Nov. 2015, pp. D447-D456. https://doi.org/10.1093%2Fnar%2Fgkv1145.

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Publisher

Oxford University Press

Journal

Nucleic Acids Research

Quartile SCImago

Quartile WOS

Impact factor

14.9

ISSN

03051048 (Print)
13624962 (Electronic)