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Results: 1 to 20 of 107

1.

NetWeAvers: an R package for integrative biological network analysis with mass spectrometry data.

McClellan EA, Moerland PD, van der Spek PJ, Stubbs AP.

Bioinformatics. 2013 Nov 15;29(22):2946-7. doi: 10.1093/bioinformatics/btt513. Epub 2013 Sep 4.

PMID:
24008417
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments.

Choi M, Chang CY, Clough T, Broudy D, Killeen T, MacLean B, Vitek O.

Bioinformatics. 2014 Sep 1;30(17):2524-6. doi: 10.1093/bioinformatics/btu305. Epub 2014 May 2.

PMID:
24794931
[PubMed - indexed for MEDLINE]
3.

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.

PMID:
19811682
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

DanteR: an extensible R-based tool for quantitative analysis of -omics data.

Taverner T, Karpievitch YV, Polpitiya AD, Brown JN, Dabney AR, Anderson GA, Smith RD.

Bioinformatics. 2012 Sep 15;28(18):2404-6. doi: 10.1093/bioinformatics/bts449. Epub 2012 Jul 19.

PMID:
22815360
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Methods and algorithms for quantitative proteomics by mass spectrometry.

Matthiesen R, Carvalho AS.

Methods Mol Biol. 2013;1007:183-217. doi: 10.1007/978-1-62703-392-3_8.

PMID:
23666727
[PubMed - indexed for MEDLINE]
6.

Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT.

Choi H, Liu G, Mellacheruvu D, Tyers M, Gingras AC, Nesvizhskii AI.

Curr Protoc Bioinformatics. 2012 Sep;Chapter 8:Unit8.15. doi: 10.1002/0471250953.bi0815s39.

PMID:
22948729
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis.

LaMarche BL, Crowell KL, Jaitly N, Petyuk VA, Shah AR, Polpitiya AD, Sandoval JD, Kiebel GR, Monroe ME, Callister SJ, Metz TO, Anderson GA, Smith RD.

BMC Bioinformatics. 2013 Feb 12;14:49. doi: 10.1186/1471-2105-14-49.

PMID:
23398735
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Proteomic parsimony through bipartite graph analysis improves accuracy and transparency.

Zhang B, Chambers MC, Tabb DL.

J Proteome Res. 2007 Sep;6(9):3549-57. Epub 2007 Aug 4.

PMID:
17676885
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

The use of edge-betweenness clustering to investigate biological function in protein interaction networks.

Dunn R, Dudbridge F, Sanderson CM.

BMC Bioinformatics. 2005 Mar 1;6:39.

PMID:
15740614
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Including shared peptides for estimating protein abundances: a significant improvement for quantitative proteomics.

Blein-Nicolas M, Xu H, de Vienne D, Giraud C, Huet S, Zivy M.

Proteomics. 2012 Sep;12(18):2797-801. doi: 10.1002/pmic.201100660.

PMID:
22833229
[PubMed - indexed for MEDLINE]
11.

A dynamic wavelet-based algorithm for pre-processing tandem mass spectrometry data.

Wang P, Yang P, Arthur J, Yang JY.

Bioinformatics. 2010 Sep 15;26(18):2242-9. doi: 10.1093/bioinformatics/btq403. Epub 2010 Jul 13.

PMID:
20628072
[PubMed - indexed for MEDLINE]
Free Article
12.

ROCS: a reproducibility index and confidence score for interaction proteomics studies.

Dazard JE, Saha S, Ewing RM.

BMC Bioinformatics. 2012 Jun 8;13:128. doi: 10.1186/1471-2105-13-128.

PMID:
22682516
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Qupe--a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments.

Albaum SP, Neuweger H, Fränzel B, Lange S, Mertens D, Trötschel C, Wolters D, Kalinowski J, Nattkemper TW, Goesmann A.

Bioinformatics. 2009 Dec 1;25(23):3128-34. doi: 10.1093/bioinformatics/btp568. Epub 2009 Oct 6.

PMID:
19808875
[PubMed - indexed for MEDLINE]
Free Article
14.

Software pipeline and data analysis for MS/MS proteomics: the trans-proteomic pipeline.

Keller A, Shteynberg D.

Methods Mol Biol. 2011;694:169-89. doi: 10.1007/978-1-60761-977-2_12.

PMID:
21082435
[PubMed - indexed for MEDLINE]
15.

IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation.

Tsou CC, Tsai CF, Tsui YH, Sudhir PR, Wang YT, Chen YJ, Chen JY, Sung TY, Hsu WL.

Mol Cell Proteomics. 2010 Jan;9(1):131-44. doi: 10.1074/mcp.M900177-MCP200. Epub 2009 Sep 13.

PMID:
19752006
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Simultaneous and exact interval estimates for the contrast of two groups based on an extremely high dimensional variable: application to mass spec data.

Park Y, Downing SR, Kim D, Hahn WC, Li C, Kantoff PW, Wei LJ.

Bioinformatics. 2007 Jun 15;23(12):1451-8. Epub 2007 Apr 25.

PMID:
17459967
[PubMed - indexed for MEDLINE]
Free Article
17.

aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data.

Rosenberger G, Ludwig C, Röst HL, Aebersold R, Malmström L.

Bioinformatics. 2014 Sep 1;30(17):2511-3. doi: 10.1093/bioinformatics/btu200. Epub 2014 Apr 20.

PMID:
24753486
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

OpenMS and TOPP: open source software for LC-MS data analysis.

Reinert K, Kohlbacher O.

Methods Mol Biol. 2010;604:201-11. doi: 10.1007/978-1-60761-444-9_14.

PMID:
20013373
[PubMed - indexed for MEDLINE]
19.

Enhanced peptide quantification using spectral count clustering and cluster abundance.

Lee S, Kwon MS, Lee HJ, Paik YK, Tang H, Lee JK, Park T.

BMC Bioinformatics. 2011 Oct 28;12:423. doi: 10.1186/1471-2105-12-423.

PMID:
22034872
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics.

Brusniak MY, Bodenmiller B, Campbell D, Cooke K, Eddes J, Garbutt A, Lau H, Letarte S, Mueller LN, Sharma V, Vitek O, Zhang N, Aebersold R, Watts JD.

BMC Bioinformatics. 2008 Dec 16;9:542. doi: 10.1186/1471-2105-9-542.

PMID:
19087345
[PubMed - indexed for MEDLINE]
Free PMC Article

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