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Items: 1 to 20 of 160

1.

PrepMS: TOF MS data graphical preprocessing tool.

Karpievitch YV, Hill EG, Smolka AJ, Morris JS, Coombes KR, Baggerly KA, Almeida JS.

Bioinformatics. 2007 Jan 15;23(2):264-5. Epub 2006 Nov 22.

2.

MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data.

Katajamaa M, Miettinen J, Oresic M.

Bioinformatics. 2006 Mar 1;22(5):634-6. Epub 2006 Jan 10.

PMID:
16403790
3.

HiRes--a tool for comprehensive assessment and interpretation of metabolomic data.

Zhao Q, Stoyanova R, Du S, Sajda P, Brown TR.

Bioinformatics. 2006 Oct 15;22(20):2562-4. Epub 2006 Aug 7.

PMID:
16895927
4.

The MiSink Plugin: Cytoscape as a graphical interface to the Database of Interacting Proteins.

Salwinski L, Eisenberg D.

Bioinformatics. 2007 Aug 15;23(16):2193-5. Epub 2007 Jun 6.

PMID:
17553858
5.

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
6.

Using BiblioSpec for creating and searching tandem MS peptide libraries.

Frewen B, MacCoss MJ.

Curr Protoc Bioinformatics. 2007 Dec;Chapter 13:Unit 13.7. doi: 10.1002/0471250953.bi1307s20.

PMID:
18428681
7.

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.

PMID:
17121776
8.

PIANA: protein interactions and network analysis.

Aragues R, Jaeggi D, Oliva B.

Bioinformatics. 2006 Apr 15;22(8):1015-7. Epub 2006 Mar 1.

PMID:
16510498
9.

OMSSAGUI: An open-source user interface component to configure and run the OMSSA search engine.

Tharakan R, Martens L, Van Eyk JE, Graham DR.

Proteomics. 2008 Jun;8(12):2376-8. doi: 10.1002/pmic.200701126.

10.

A database application for pre-processing, storage and comparison of mass spectra derived from patients and controls.

Titulaer MK, Siccama I, Dekker LJ, van Rijswijk AL, Heeren RM, Sillevis Smitt PA, Luider TM.

BMC Bioinformatics. 2006 Sep 5;7:403.

11.

DBToolkit: processing protein databases for peptide-centric proteomics.

Martens L, Vandekerckhove J, Gevaert K.

Bioinformatics. 2005 Sep 1;21(17):3584-5. Epub 2005 Jul 19.

PMID:
16030071
12.

TOPP--the OpenMS proteomics pipeline.

Kohlbacher O, Reinert K, Gröpl C, Lange E, Pfeifer N, Schulz-Trieglaff O, Sturm M.

Bioinformatics. 2007 Jan 15;23(2):e191-7.

PMID:
17237091
13.

NGSView: an extensible open source editor for next-generation sequencing data.

Arner E, Hayashizaki Y, Daub CO.

Bioinformatics. 2010 Jan 1;26(1):125-6. doi: 10.1093/bioinformatics/btp611. Epub 2009 Oct 24.

14.

pFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry.

Wang LH, Li DQ, Fu Y, Wang HP, Zhang JF, Yuan ZF, Sun RX, Zeng R, He SM, Gao W.

Rapid Commun Mass Spectrom. 2007;21(18):2985-91.

PMID:
17702057
15.

Quality control and preprocessing of metagenomic datasets.

Schmieder R, Edwards R.

Bioinformatics. 2011 Mar 15;27(6):863-4. doi: 10.1093/bioinformatics/btr026. Epub 2011 Jan 28.

16.
17.

PROTEIOS: an open source proteomics initiative.

Gärdén P, Alm R, Häkkinen J.

Bioinformatics. 2005 May 1;21(9):2085-7. Epub 2005 Feb 3.

PMID:
15691852
18.

A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS.

Bellew M, Coram M, Fitzgibbon M, Igra M, Randolph T, Wang P, May D, Eng J, Fang R, Lin C, Chen J, Goodlett D, Whiteaker J, Paulovich A, McIntosh M.

Bioinformatics. 2006 Aug 1;22(15):1902-9. Epub 2006 Jun 9.

PMID:
16766559
19.

eF-site and PDBjViewer: database and viewer for protein functional sites.

Kinoshita K, Nakamura H.

Bioinformatics. 2004 May 22;20(8):1329-30. Epub 2004 Feb 10.

PMID:
14871866
20.

MzJava: An open source library for mass spectrometry data processing.

Horlacher O, Nikitin F, Alocci D, Mariethoz J, Müller M, Lisacek F.

J Proteomics. 2015 Nov 3;129:63-70. doi: 10.1016/j.jprot.2015.06.013. Epub 2015 Jun 30.

PMID:
26141507

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