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An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ.

Siepen JA, Swainston N, Jones AR, Hart SR, Hermjakob H, Jones P, Hubbard SJ.

Proteome Sci. 2007 Feb 1;5:4. doi: 10.1186/1477-5956-5-4.


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.


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.


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.


An automated proteomic data analysis workflow for mass spectrometry.

Pendarvis K, Kumar R, Burgess SC, Nanduri B.

BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S17. doi: 10.1186/1471-2105-10-S11-S17.


Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective.

Perez-Riverol Y, Wang R, Hermjakob H, Müller M, Vesada V, Vizcaíno JA.

Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):63-76. doi: 10.1016/j.bbapap.2013.02.032. Epub 2013 Mar 1. Review.


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.


ms-data-core-api: an open-source, metadata-oriented library for computational proteomics.

Perez-Riverol Y, Uszkoreit J, Sanchez A, Ternent T, Del Toro N, Hermjakob H, Vizcaíno JA, Wang R.

Bioinformatics. 2015 Sep 1;31(17):2903-5. doi: 10.1093/bioinformatics/btv250. Epub 2015 Apr 24.


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.


A uniform proteomics MS/MS analysis platform utilizing open XML file formats.

Keller A, Eng J, Zhang N, Li XJ, Aebersold R.

Mol Syst Biol. 2005;1:2005.0017. Epub 2005 Aug 2.


MASCOT HTML and XML parser: an implementation of a novel object model for protein identification data.

Yang CG, Granite SJ, Van Eyk JE, Winslow RL.

Proteomics. 2006 Nov;6(21):5688-93.

12. IO Framework: reading and writing multiple proteomics data formats.

Falkner JA, Falkner JW, Andrews PC.

Bioinformatics. 2007 Jan 15;23(2):262-3. Epub 2006 Nov 22.


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.


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.


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.


Precise protein quantification based on peptide quantification using iTRAQ.

Boehm AM, Pütz S, Altenhöfer D, Sickmann A, Falk M.

BMC Bioinformatics. 2007 Jun 21;8:214.


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.


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.


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.


jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.

Griss J, Reisinger F, Hermjakob H, Vizcaíno JA.

Proteomics. 2012 Mar;12(6):795-8. doi: 10.1002/pmic.201100578.

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