PRoteomics IDEntifications database

Abbreviation:PRIDE

Recommended

General Information

The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence.

Homepage http://www.ebi.ac.uk/pride/

Countries that developed this resource Austria , Belgium , Croatia , Czech Republic , Denmark , Finland , France , Germany , Greece , Hungary , Iceland , Israel , Italy , Lithuania , Luxembourg , Malta , Montenegro , Netherlands , Norway , Portugal , Republic of Ireland , Slovakia , Spain , Sweden , Switzerland , United Kingdom

Created in 2004

Taxonomic range

All

Knowledge Domains

Subjects

In the following recommendations:

How to cite this record FAIRsharing.org: PRIDE; PRoteomics IDEntifications database; DOI: https://doi.org/10.25504/FAIRsharing.e1byny; Last edited: Feb. 10, 2020, 2:59 p.m.; Last accessed: Feb 18 2020 4:05 p.m.

Publication for citation The PRIDE database and related tools and resources in 2019: improving support for quantification data. Perez-Riverol Y,Csordas A,Bai J,Bernal-Llinares M,Hewapathirana S,Kundu DJ,Inuganti A,Griss J,Mayer G,Eisenacher M,Perez E,Uszkoreit J,Pfeuffer J,Sachsenberg T,Yilmaz S,Tiwary S,Cox J,Audain E,Walzer M,Jarnuczak AF,Ternent T,Brazma A,Vizcaino JA; Nucleic Acids Res ; 2018; 10.1093/nar/gky1106;

This record is maintained by prideebi

Record updated: Feb. 10, 2020, 2:59 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.e1byny' by 'The FAIRsharing Team' at 14:59, 10 Feb 2020 (approved):

	'supportLinks' has been modified:
		Before:
			FAQ|http://www.ebi.ac.uk/pride/help/archive/faq
			TeSS training|https://tess.elixir-europe.org/materials/pride-and-proteomexchange-webinar
			TeSS training|https://tess.elixir-europe.org/materials/pride-and-proteomexchange-webinar
			help|http://www.ebi.ac.uk/pride/help/archive
			training|https://www.ebi.ac.uk/training/online/course/proteomexchange-submissions-pride
			twitter|@pride_ebi
		After:
			FAQ|http://www.ebi.ac.uk/pride/help/archive/faq
			TeSS training|https://tess.elixir-europe.org/materials/pride-and-proteomexchange-webinar
			TeSS training|https://tess.elixir-europe.org/materials/pride-and-proteomexchange-webinar
			help|http://www.ebi.ac.uk/pride/help/archive
			help|https://www.ebi.ac.uk/pride/markdownpage/documentationpage
			training|https://www.ebi.ac.uk/training/online/course/proteomexchange-submissions-pride
			twitter|@pride_ebi
		Added:
			help|https://www.ebi.ac.uk/pride/markdownpage/documentationpage
		Removed:

	'tools' has been modified:
		Before:
			PRIDE Inspector||https://github.com/PRIDE-Toolsuite/pride-inspector
			PRIDE Toolsuite||https://github.com/PRIDE-Toolsuite
		After:
			PRIDE Inspector||https://github.com/PRIDE-Toolsuite/pride-inspector
			PRIDE Utilities||https://www.ebi.ac.uk/pride/markdownpage/prideutilities
			PRIDE Submission Tool||https://www.ebi.ac.uk/pride/markdownpage/pridesubmissiontool
		Added:
			PRIDE Utilities||https://www.ebi.ac.uk/pride/markdownpage/prideutilities
			PRIDE Submission Tool||https://www.ebi.ac.uk/pride/markdownpage/pridesubmissiontool
		Removed:
			PRIDE Toolsuite||https://github.com/PRIDE-Toolsuite

	'publications' has been modified:
		Before:
			PRIDE: a public repository of protein and peptide identifications for the proteomics community.|Jones P., Ct RG., Martens L., Quinn AF., Taylor CF., Derache W., Hermjakob H., Apweiler R., |Nucleic Acids Res.|2006
			The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013.|Vizcano JA., Ct RG., Csordas A., Dianes JA., Fabregat A., Foster JM., Griss J., Alpi E., Birim M., Contell J., O'Kelly G., Schoenegger A., Ovelleiro D., Prez-Riverol Y., Reisinger F., Ros D., Wang R., Hermjakob H., |Nucleic Acids Res.|2013
			ProteomeXchange provides globally coordinated proteomics data submission and dissemination.|Vizcano JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ros D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolom S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H.|Nat Biotechnol.|2014
			PRIDE: the proteomics identifications database.|Martens L,Hermjakob H,Jones P,Adamski M,Taylor C,States D,Gevaert K,Vandekerckhove J,Apweiler R|Proteomics|2005
			PRIDE: new developments and new datasets.|Jones P,Cote RG,Cho SY,Klie S,Martens L,Quinn AF,Thorneycroft D,Hermjakob H|Nucleic Acids Res|2007
			Using the Proteomics Identifications Database (PRIDE).|Martens L,Jones P,Cote R|Curr Protoc Bioinformatics|2008
			How to submit MS proteomics data to ProteomeXchange via the PRIDE database.|Ternent T,Csordas A,Qi D,Gomez-Baena G,Beynon RJ,Jones AR,Hermjakob H,Vizcaino JA|Proteomics|2014
			2016 update of the PRIDE database and its related tools.|Vizcaino JA,Csordas A,del-Toro N,Dianes JA,Griss J,Lavidas I,Mayer G,Perez-Riverol Y,Reisinger F,Ternent T,Xu QW,Wang R,Hermjakob H|Nucleic Acids Res|2015
		After:
			PRIDE: a public repository of protein and peptide identifications for the proteomics community.|Jones P., Ct RG., Martens L., Quinn AF., Taylor CF., Derache W., Hermjakob H., Apweiler R., |Nucleic Acids Res.|2006
			The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013.|Vizcano JA., Ct RG., Csordas A., Dianes JA., Fabregat A., Foster JM., Griss J., Alpi E., Birim M., Contell J., O'Kelly G., Schoenegger A., Ovelleiro D., Prez-Riverol Y., Reisinger F., Ros D., Wang R., Hermjakob H., |Nucleic Acids Res.|2013
			ProteomeXchange provides globally coordinated proteomics data submission and dissemination.|Vizcano JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ros D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolom S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H.|Nat Biotechnol.|2014
			PRIDE: the proteomics identifications database.|Martens L,Hermjakob H,Jones P,Adamski M,Taylor C,States D,Gevaert K,Vandekerckhove J,Apweiler R|Proteomics|2005
			PRIDE: new developments and new datasets.|Jones P,Cote RG,Cho SY,Klie S,Martens L,Quinn AF,Thorneycroft D,Hermjakob H|Nucleic Acids Res|2007
			Using the Proteomics Identifications Database (PRIDE).|Martens L,Jones P,Cote R|Curr Protoc Bioinformatics|2008
			How to submit MS proteomics data to ProteomeXchange via the PRIDE database.|Ternent T,Csordas A,Qi D,Gomez-Baena G,Beynon RJ,Jones AR,Hermjakob H,Vizcaino JA|Proteomics|2014
			2016 update of the PRIDE database and its related tools.|Vizcaino JA,Csordas A,del-Toro N,Dianes JA,Griss J,Lavidas I,Mayer G,Perez-Riverol Y,Reisinger F,Ternent T,Xu QW,Wang R,Hermjakob H|Nucleic Acids Res|2015
			The PRIDE database and related tools and resources in 2019: improving support for quantification data.|Perez-Riverol Y,Csordas A,Bai J,Bernal-Llinares M,Hewapathirana S,Kundu DJ,Inuganti A,Griss J,Mayer G,Eisenacher M,Perez E,Uszkoreit J,Pfeuffer J,Sachsenberg T,Yilmaz S,Tiwary S,Cox J,Audain E,Walzer M,Jarnuczak AF,Ternent T,Brazma A,Vizcaino JA|Nucleic Acids Res|2018
		Added:
			The PRIDE database and related tools and resources in 2019: improving support for quantification data.|Perez-Riverol Y,Csordas A,Bai J,Bernal-Llinares M,Hewapathirana S,Kundu DJ,Inuganti A,Griss J,Mayer G,Eisenacher M,Perez E,Uszkoreit J,Pfeuffer J,Sachsenberg T,Yilmaz S,Tiwary S,Cox J,Audain E,Walzer M,Jarnuczak AF,Ternent T,Brazma A,Vizcaino JA|Nucleic Acids Res|2018
		Removed:

	'dataProcesses' has been modified:
		Before:
			Browse
			Submit
			Download
		After:
			Search Archive
			Submit
			Download
			Search Spectra
			Peptidome
			Search Spectral Libraries
		Added:
			Search Archive
			Search Spectra
			Peptidome
			Search Spectral Libraries
		Removed:
			Browse

	'countries' has been modified:
		Before:
			European Union
		After:
			Austria
			Belgium
			Croatia
			Czech Republic
			Denmark
			Finland
			France
			Germany
			Greece
			Hungary
			Iceland
			Israel
			Italy
			Lithuania
			Luxembourg
			Malta
			Montenegro
			Netherlands
			Norway
			Portugal
			Republic of Ireland
			Slovakia
			Spain
			Sweden
			Switzerland
			United Kingdom
		Added:
			Austria
			Belgium
			Croatia
			Czech Republic
			Denmark
			Finland
			France
			Germany
			Greece
			Hungary
			Iceland
			Israel
			Italy
			Lithuania
			Luxembourg
			Malta
			Montenegro
			Netherlands
			Norway
			Portugal
			Republic of Ireland
			Slovakia
			Spain
			Sweden
			Switzerland
			United Kingdom
		Removed:
			European Union

Edits to 'https://fairsharing.org/FAIRsharing.e1byny' by 'The FAIRsharing Team' at 13:43, 09 Jan 2019 (approved):

	'supportLinks' has been modified:
		Before:
			FAQ|http://www.ebi.ac.uk/pride/help/archive/faq
			TeSS training|https://tess.elixir-europe.org/materials/pride-and-proteomexchange-webinar
			help|http://www.ebi.ac.uk/pride/help/archive
			tess training|https://tess.elixir-europe.org/materials/pride-and-proteomexchange-webinar
			training|http://www.ebi.ac.uk/training
			twitter|@pride_ebi
		After:
			FAQ|http://www.ebi.ac.uk/pride/help/archive/faq
			TeSS training|https://tess.elixir-europe.org/materials/pride-and-proteomexchange-webinar
			TeSS training|https://tess.elixir-europe.org/materials/pride-and-proteomexchange-webinar
			help|http://www.ebi.ac.uk/pride/help/archive
			training|https://www.ebi.ac.uk/training/online/course/proteomexchange-submissions-pride
			twitter|@pride_ebi
		Added:
			training|https://www.ebi.ac.uk/training/online/course/proteomexchange-submissions-pride
		Removed:
			tess training|https://tess.elixir-europe.org/materials/pride-and-proteomexchange-webinar
			training|http://www.ebi.ac.uk/training

	'tools' has been modified:
		Before:
			PRIDE Inspector||https://github.com/PRIDE-Toolsuite/pride-inspector
			PRIDE Converter|v2.0.21|https://code.google.com/archive/p/pride-converter-2/
		After:
			PRIDE Inspector||https://github.com/PRIDE-Toolsuite/pride-inspector
			PRIDE Toolsuite||https://github.com/PRIDE-Toolsuite
		Added:
			PRIDE Toolsuite||https://github.com/PRIDE-Toolsuite
		Removed:
			PRIDE Converter|v2.0.21|https://code.google.com/archive/p/pride-converter-2/

	'organizations' has been modified:
		Before:
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Funds
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
			The Wellcome Trust, UK|https://wellcome.ac.uk/|Funds
		After:
			European Molecular Biology Laboratory (EMBL), Heidelberg, Germany|http://www.embl.org|Funds
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
			The Wellcome Trust, UK|https://wellcome.ac.uk/|Funds
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
		Added:
			European Molecular Biology Laboratory (EMBL), Heidelberg, Germany|http://www.embl.org|Funds
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
		Removed:
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Funds
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains

Edits to 'https://fairsharing.org/FAIRsharing.e1byny' by 'The FAIRsharing Team' at 11:29, 07 Aug 2018 (approved):

	'supportLinks' has been modified:
		Before:
			FAQ|http://www.ebi.ac.uk/pride/help/archive/faq
			TeSS training|https://tess.elixir-europe.org/materials/pride-and-proteomexchange-webinar
			help|http://www.ebi.ac.uk/pride/help/archive
			training|http://www.ebi.ac.uk/training
			twitter|@pride_ebi
		After:
			FAQ|http://www.ebi.ac.uk/pride/help/archive/faq
			TeSS training|https://tess.elixir-europe.org/materials/pride-and-proteomexchange-webinar
			help|http://www.ebi.ac.uk/pride/help/archive
			tess training|https://tess.elixir-europe.org/materials/pride-and-proteomexchange-webinar
			training|http://www.ebi.ac.uk/training
			twitter|@pride_ebi
		Added:
			tess training|https://tess.elixir-europe.org/materials/pride-and-proteomexchange-webinar
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.e1byny' by 'The FAIRsharing Team' at 22:37, 02 Aug 2018 (approved):

	'organizations' has been modified:
		Before:
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
		After:
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom|https://www.ebi.ac.uk/|Funds
			The Wellcome Trust, UK|https://wellcome.ac.uk|Funds
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
		Added:
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom|https://www.ebi.ac.uk/|Funds
			The Wellcome Trust, UK|https://wellcome.ac.uk|Funds
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
		Removed:

	'grants' has been modified:
		Before:
		After:
			BB/I00095X/1
			BB/K01997X/1
			BB/L024225/1
			WT101477MA
		Added:
			BB/I00095X/1
			BB/K01997X/1
			BB/L024225/1
			WT101477MA
		Removed:

	'publications' has been modified:
		Before:
			PRIDE: a public repository of protein and peptide identifications for the proteomics community.|Jones P., Ct RG., Martens L., Quinn AF., Taylor CF., Derache W., Hermjakob H., Apweiler R., |Nucleic Acids Res.|2006
			The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013.|Vizcano JA., Ct RG., Csordas A., Dianes JA., Fabregat A., Foster JM., Griss J., Alpi E., Birim M., Contell J., O'Kelly G., Schoenegger A., Ovelleiro D., Prez-Riverol Y., Reisinger F., Ros D., Wang R., Hermjakob H., |Nucleic Acids Res.|2013
			ProteomeXchange provides globally coordinated proteomics data submission and dissemination.|Vizcano JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ros D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolom S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H.|Nat Biotechnol.|2014
			PRIDE: the proteomics identifications database.|Martens L,Hermjakob H,Jones P,Adamski M,Taylor C,States D,Gevaert K,Vandekerckhove J,Apweiler R|Proteomics|2005
			PRIDE: new developments and new datasets.|Jones P,Cote RG,Cho SY,Klie S,Martens L,Quinn AF,Thorneycroft D,Hermjakob H|Nucleic Acids Res|2007
			Using the Proteomics Identifications Database (PRIDE).|Martens L,Jones P,Cote R|Curr Protoc Bioinformatics|2008
		After:
			PRIDE: a public repository of protein and peptide identifications for the proteomics community.|Jones P., Ct RG., Martens L., Quinn AF., Taylor CF., Derache W., Hermjakob H., Apweiler R., |Nucleic Acids Res.|2006
			The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013.|Vizcano JA., Ct RG., Csordas A., Dianes JA., Fabregat A., Foster JM., Griss J., Alpi E., Birim M., Contell J., O'Kelly G., Schoenegger A., Ovelleiro D., Prez-Riverol Y., Reisinger F., Ros D., Wang R., Hermjakob H., |Nucleic Acids Res.|2013
			ProteomeXchange provides globally coordinated proteomics data submission and dissemination.|Vizcano JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ros D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolom S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H.|Nat Biotechnol.|2014
			PRIDE: the proteomics identifications database.|Martens L,Hermjakob H,Jones P,Adamski M,Taylor C,States D,Gevaert K,Vandekerckhove J,Apweiler R|Proteomics|2005
			PRIDE: new developments and new datasets.|Jones P,Cote RG,Cho SY,Klie S,Martens L,Quinn AF,Thorneycroft D,Hermjakob H|Nucleic Acids Res|2007
			Using the Proteomics Identifications Database (PRIDE).|Martens L,Jones P,Cote R|Curr Protoc Bioinformatics|2008
			How to submit MS proteomics data to ProteomeXchange via the PRIDE database.|Ternent T,Csordas A,Qi D,Gomez-Baena G,Beynon RJ,Jones AR,Hermjakob H,Vizcaino JA|Proteomics|2014
			2016 update of the PRIDE database and its related tools.|Vizcaino JA,Csordas A,del-Toro N,Dianes JA,Griss J,Lavidas I,Mayer G,Perez-Riverol Y,Reisinger F,Ternent T,Xu QW,Wang R,Hermjakob H|Nucleic Acids Res|2015
		Added:
			How to submit MS proteomics data to ProteomeXchange via the PRIDE database.|Ternent T,Csordas A,Qi D,Gomez-Baena G,Beynon RJ,Jones AR,Hermjakob H,Vizcaino JA|Proteomics|2014
			2016 update of the PRIDE database and its related tools.|Vizcaino JA,Csordas A,del-Toro N,Dianes JA,Griss J,Lavidas I,Mayer G,Perez-Riverol Y,Reisinger F,Ternent T,Xu QW,Wang R,Hermjakob H|Nucleic Acids Res|2015
		Removed:

	'contact' has been modified:
		Before: 
		After: General contact

In Collections

Data Citation Implementation

ELIXIR Core Data Resources and Deposition Databases

Support

General

FAQ	PRIDE FAQ
help	Help Pages
help	Documentation
training	PRIDE Training
twitter	@pride_ebi

Additional Information

Contact

General contact

TeSS training resources

Pride and proteomexchange webinar

PRIDE and ProteomeXchange: webinar

Tools

PRIDE Inspector	https://github.com/PRIDE-Toolsuite/pride-inspector
PRIDE Utilities	https://www.ebi.ac.uk/pride/markdownpage/prideutilities
PRIDE Submission Tool	https://www.ebi.ac.uk/pride/markdownpage/pridesubmissiontool

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0

Data Release

Download

ftp://ftp.pride.ebi.ac.uk/pride/data/archive

Data Curation

Submit

http://www.ebi.ac.uk/pride/help/archive/submission

Data Access

Search Archive	https://www.ebi.ac.uk/pride/
Search Spectra	https://www.ebi.ac.uk/pride/archive/spectra
Peptidome	https://www.ebi.ac.uk/pride/peptidome
Search Spectral Libraries	https://www.ebi.ac.uk/pride/spectrumlibrary

REST Web Services

PRIDE Archive RESTful web service API

http://www.ebi.ac.uk/pride/ws/archive/

Publications

PRIDE: a public repository of protein and peptide identifications for the proteomics community.

Jones P., Côté RG., Martens L., Quinn AF., Taylor CF., Derache W., Hermjakob H., Apweiler R.,
Nucleic Acids Res. 2006