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Items: 1 to 20 of 89

1.

PRIDE Inspector: a tool to visualize and validate MS proteomics data.

Wang R, Fabregat A, Ríos D, Ovelleiro D, Foster JM, Côté RG, Griss J, Csordas A, Perez-Riverol Y, Reisinger F, Hermjakob H, Martens L, Vizcaíno JA.

Nat Biotechnol. 2012 Feb 8;30(2):135-7. doi: 10.1038/nbt.2112. No abstract available.

2.

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.

3.

Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories.

Martens L, Nesvizhskii AI, Hermjakob H, Adamski M, Omenn GS, Vandekerckhove J, Gevaert K.

Proteomics. 2005 Aug;5(13):3501-5.

PMID:
16041670
4.

PRIDE Converter: making proteomics data-sharing easy.

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

Nat Biotechnol. 2009 Jul;27(7):598-9. doi: 10.1038/nbt0709-598. No abstract available.

PMID:
19587657
5.

MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data.

Hartler J, Thallinger GG, Stocker G, Sturn A, Burkard TR, Körner E, Rader R, Schmidt A, Mechtler K, Trajanoski Z.

BMC Bioinformatics. 2007 Jun 13;8:197.

6.

Using the Proteomics Identifications Database (PRIDE).

Martens L, Jones P, Côté R.

Curr Protoc Bioinformatics. 2008 Mar;Chapter 13:Unit 13.8. doi: 10.1002/0471250953.bi1308s21.

PMID:
18428683
7.

A grid environment for high-throughput proteomics.

Cannataro M, Barla A, Flor R, Jurman G, Merler S, Paoli S, Tradigo G, Veltri P, Furlanello C.

IEEE Trans Nanobioscience. 2007 Jun;6(2):117-23.

PMID:
17695745
8.

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.

9.

ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics.

Helsens K, Colaert N, Barsnes H, Muth T, Flikka K, Staes A, Timmerman E, Wortelkamp S, Sickmann A, Vandekerckhove J, Gevaert K, Martens L.

Proteomics. 2010 Mar;10(6):1261-4. doi: 10.1002/pmic.200900409. Erratum in: Proteomics.2010 Jul;10(13):2560.

PMID:
20058248
10.

A bioinformatics perspective on proteomics: data storage, analysis, and integration.

Kremer A, Schneider R, Terstappen GC.

Biosci Rep. 2005 Feb-Apr;25(1-2):95-106. Review.

PMID:
16222422
11.

Data hoarding is harming proteomics.

Noble WS.

Nat Biotechnol. 2004 Oct;22(10):1209; discussion 1209. No abstract available.

PMID:
15470451
12.

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
13.

Visual analysis of gel-free proteome data.

Linsen L, Löcherbach J, Berth M, Becher D, Bernhardt J.

IEEE Trans Vis Comput Graph. 2006 Jul-Aug;12(4):497-508.

PMID:
16805259
14.

ProteomeCommons.org 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.

15.

PepSeeker: mining information from proteomic data.

Siepen JA, Selley JN, Hubbard SJ.

Methods Mol Biol. 2008;484:319-32. doi: 10.1007/978-1-59745-398-1_21.

PMID:
18592189
16.

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.

17.

Information management for proteomics: a perspective.

Wilkins MR, Arthur JW, Junius FK, Harrison MJ, Traini MD, Bizannes P, Doggett PE, McDonald W.

Expert Rev Proteomics. 2008 Oct;5(5):663-78. doi: 10.1586/14789450.5.5.663. Review.

PMID:
18937557
18.

SPLASH: systematic proteomics laboratory analysis and storage hub.

Lo SL, You T, Lin Q, Joshi SB, Chung MC, Hew CL.

Proteomics. 2006 Mar;6(6):1758-69.

PMID:
16456885
19.

Bioinformatics support for high-throughput proteomics.

Wilke A, Rückert C, Bartels D, Dondrup M, Goesmann A, Hüser AT, Kespohl S, Linke B, Mahne M, McHardy A, Pühler A, Meyer F.

J Biotechnol. 2003 Dec 19;106(2-3):147-56.

PMID:
14651857
20.

Installation and use of the Computational Proteomics Analysis System (CPAS).

Myers T, Law W, Eng JK, McIntosh M.

Curr Protoc Bioinformatics. 2007 Jun;Chapter 13:Unit 13.5. doi: 10.1002/0471250953.bi1305s18.

PMID:
18428786
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