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Items: 13

1.

The mzIdentML data standard for mass spectrometry-based proteomics results.

Jones AR, Eisenacher M, Mayer G, Kohlbacher O, Siepen J, Hubbard SJ, Selley JN, Searle BC, Shofstahl J, Seymour SL, Julian R, Binz PA, Deutsch EW, Hermjakob H, Reisinger F, Griss J, Vizcaíno JA, Chambers M, Pizarro A, Creasy D.

Mol Cell Proteomics. 2012 Jul;11(7):M111.014381. doi: 10.1074/mcp.M111.014381. Epub 2012 Feb 27.

2.

FDRAnalysis: a tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines.

Wedge DC, Krishna R, Blackhurst P, Siepen JA, Jones AR, Hubbard SJ.

J Proteome Res. 2011 Apr 1;10(4):2088-94. doi: 10.1021/pr101157s. Epub 2011 Feb 21.

3.

Investigating protein isoforms via proteomics: a feasibility study.

Blakeley P, Siepen JA, Lawless C, Hubbard SJ.

Proteomics. 2010 Mar;10(6):1127-40. doi: 10.1002/pmic.200900445.

4.

Getting a grip on proteomics data - Proteomics Data Collection (ProDaC).

Eisenacher M, Martens L, Hardt T, Kohl M, Barsnes H, Helsens K, Häkkinen J, Levander F, Aebersold R, Vandekerckhove J, Dunn MJ, Lisacek F, Siepen JA, Hubbard SJ, Binz PA, Blüggel M, Thiele H, Cottrell J, Meyer HE, Apweiler R, Stephan C.

Proteomics. 2009 Aug;9(15):3928-33. doi: 10.1002/pmic.200900247.

PMID:
19637238
5.

Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines.

Jones AR, Siepen JA, Hubbard SJ, Paton NW.

Proteomics. 2009 Mar;9(5):1220-9. doi: 10.1002/pmic.200800473.

6.

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
7.

ISPIDER Central: an integrated database web-server for proteomics.

Siepen JA, Belhajjame K, Selley JN, Embury SM, Paton NW, Goble CA, Oliver SG, Stevens R, Zamboulis L, Martin N, Poulovassillis A, Jones P, Côté R, Hermjakob H, Pentony MM, Jones DT, Orengo CA, Hubbard SJ.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W485-90. doi: 10.1093/nar/gkn196. Epub 2008 Apr 25.

8.

Capture and analysis of quantitative proteomic data.

Lau KW, Jones AR, Swainston N, Siepen JA, Hubbard SJ.

Proteomics. 2007 Aug;7(16):2787-99. Review.

9.

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.

10.

Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics.

Siepen JA, Keevil EJ, Knight D, Hubbard SJ.

J Proteome Res. 2007 Jan;6(1):399-408.

11.

PepSeeker: a database of proteome peptide identifications for investigating fragmentation patterns.

McLaughlin T, Siepen JA, Selley J, Lynch JA, Lau KW, Yin H, Gaskell SJ, Hubbard SJ.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D649-54.

12.

Beta edge strands in protein structure prediction and aggregation.

Siepen JA, Radford SE, Westhead DR.

Protein Sci. 2003 Oct;12(10):2348-59.

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