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Items: 1 to 20 of 197

1.

The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium.

Côté RG, Griss J, Dianes JA, Wang R, Wright JC, van den Toorn HW, van Breukelen B, Heck AJ, Hulstaert N, Martens L, Reisinger F, Csordas A, Ovelleiro D, Perez-Rivevol Y, Barsnes H, Hermjakob H, Vizcaíno JA.

Mol Cell Proteomics. 2012 Dec;11(12):1682-9. doi: 10.1074/mcp.O112.021543. Epub 2012 Sep 4.

2.

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets.

Perez-Riverol Y, Xu QW, Wang R, Uszkoreit J, Griss J, Sanchez A, Reisinger F, Csordas A, Ternent T, Del-Toro N, Dianes JA, Eisenacher M, Hermjakob H, Vizcaíno JA.

Mol Cell Proteomics. 2016 Jan;15(1):305-17. doi: 10.1074/mcp.O115.050229. Epub 2015 Nov 6.

3.

Submitting proteomics data to PRIDE using PRIDE Converter.

Barsnes H, Vizcaíno JA, Reisinger F, Eidhammer I, Martens L.

Methods Mol Biol. 2011;694:237-53. doi: 10.1007/978-1-60761-977-2_16.

PMID:
21082439
4.

2016 update of the PRIDE database and its related tools.

Vizcaíno 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. 2016 Jan 4;44(D1):D447-56. doi: 10.1093/nar/gkv1145. Epub 2015 Nov 2. Erratum in: Nucleic Acids Res. 2016 Dec 15;44(22):11033.

5.

The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013.

Vizcaíno JA, Côté RG, Csordas A, Dianes JA, Fabregat A, Foster JM, Griss J, Alpi E, Birim M, Contell J, O'Kelly G, Schoenegger A, Ovelleiro D, Pérez-Riverol Y, Reisinger F, Ríos D, Wang R, Hermjakob H.

Nucleic Acids Res. 2013 Jan;41(Database issue):D1063-9. doi: 10.1093/nar/gks1262. Epub 2012 Nov 29.

6.

A guide to the Proteomics Identifications Database proteomics data repository.

Vizcaíno JA, Côté R, Reisinger F, Foster JM, Mueller M, Rameseder J, Hermjakob H, Martens L.

Proteomics. 2009 Sep;9(18):4276-83. doi: 10.1002/pmic.200900402.

7.

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 Jan 1;34(Database issue):D659-63.

8.

Using the PRIDE proteomics identifications database for knowledge discovery and data analysis.

Jones P, Martens L.

Methods Mol Biol. 2010;604:297-307. doi: 10.1007/978-1-60761-444-9_20.

PMID:
20013379
9.

ProCon - PROteomics CONversion tool.

Mayer G, Stephan C, Meyer HE, Kohl M, Marcus K, Eisenacher M.

J Proteomics. 2015 Nov 3;129:56-62. doi: 10.1016/j.jprot.2015.06.015. Epub 2015 Jul 13.

PMID:
26182917
10.

How to submit MS proteomics data to ProteomeXchange via the PRIDE database.

Ternent T, Csordas A, Qi D, Gómez-Baena G, Beynon RJ, Jones AR, Hermjakob H, Vizcaíno JA.

Proteomics. 2014 Oct;14(20):2233-41. doi: 10.1002/pmic.201400120. Epub 2014 Aug 21.

11.

PRIDEViewer: a novel user-friendly interface to visualize PRIDE XML files.

Medina-Aunon JA, Carazo JM, Albar JP.

Proteomics. 2011 Jan;11(2):334-7. doi: 10.1002/pmic.201000448. Epub 2010 Dec 17.

PMID:
21204261
12.

The PRIDE proteomics identifications database: data submission, query, and dataset comparison.

Jones P, Côté R.

Methods Mol Biol. 2008;484:287-303. doi: 10.1007/978-1-59745-398-1_19.

PMID:
18592187
13.

jmzTab: a java interface to the mzTab data standard.

Xu QW, Griss J, Wang R, Jones AR, Hermjakob H, Vizcaíno JA.

Proteomics. 2014 Jun;14(11):1328-32. doi: 10.1002/pmic.201300560. Epub 2014 Apr 29.

14.

PRIDE: new developments and new datasets.

Jones P, Côté RG, Cho SY, Klie S, Martens L, Quinn AF, Thorneycroft D, Hermjakob H.

Nucleic Acids Res. 2008 Jan;36(Database issue):D878-83. Epub 2007 Nov 22.

15.

PRIDE: Data submission and analysis.

Vizcaíno JA, Reisinger F, Côté R, Martens L.

Curr Protoc Protein Sci. 2010 Apr;Chapter 25:Unit 25.4. doi: 10.1002/0471140864.ps2504s60.

PMID:
20393974
16.

The Proteomics Identifications database: 2010 update.

Vizcaíno JA, Côté R, Reisinger F, Barsnes H, Foster JM, Rameseder J, Hermjakob H, Martens L.

Nucleic Acids Res. 2010 Jan;38(Database issue):D736-42. doi: 10.1093/nar/gkp964. Epub 2009 Nov 11.

17.

Introducing the PRIDE Archive RESTful web services.

Reisinger F, del-Toro N, Ternent T, Hermjakob H, Vizcaíno JA.

Nucleic Acids Res. 2015 Jul 1;43(W1):W599-604. doi: 10.1093/nar/gkv382. Epub 2015 Apr 22.

18.

Pride-asap: automatic fragment ion annotation of identified PRIDE spectra.

Hulstaert N, Reisinger F, Rameseder J, Barsnes H, Vizcaíno JA, Martens L.

J Proteomics. 2013 Dec 16;95:89-92. doi: 10.1016/j.jprot.2013.04.011. Epub 2013 Apr 17.

19.

Using the PRIDE Database and ProteomeXchange for Submitting and Accessing Public Proteomics Datasets.

Jarnuczak AF, Vizcaíno JA.

Curr Protoc Bioinformatics. 2017 Sep 13;59:13.31.1-13.31.12. doi: 10.1002/cpbi.30.

PMID:
28902400
20.

The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience.

Griss J, Jones AR, Sachsenberg T, Walzer M, Gatto L, Hartler J, Thallinger GG, Salek RM, Steinbeck C, Neuhauser N, Cox J, Neumann S, Fan J, Reisinger F, Xu QW, Del Toro N, Pérez-Riverol Y, Ghali F, Bandeira N, Xenarios I, Kohlbacher O, Vizcaíno JA, Hermjakob H.

Mol Cell Proteomics. 2014 Oct;13(10):2765-75. doi: 10.1074/mcp.O113.036681. Epub 2014 Jun 30.

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