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Items: 1 to 20 of 95

1.

Supporting tool suite for production proteomics.

Ma ZQ, Tabb DL, Burden J, Chambers MC, Cox MB, Cantrell MJ, Ham AJ, Litton MD, Oreto MR, Schultz WC, Sobecki SM, Tsui TY, Wernke GR, Liebler DC.

Bioinformatics. 2011 Nov 15;27(22):3214-5. doi: 10.1093/bioinformatics/btr544. Epub 2011 Sep 29.

2.

A common open representation of mass spectrometry data and its application to proteomics research.

Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R.

Nat Biotechnol. 2004 Nov;22(11):1459-66.

PMID:
15529173
3.

ProteinQuant Suite: a bundle of automated software tools for label-free quantitative proteomics.

Mann B, Madera M, Sheng Q, Tang H, Mechref Y, Novotny MV.

Rapid Commun Mass Spectrom. 2008 Dec;22(23):3823-34. doi: 10.1002/rcm.3781.

PMID:
18985620
4.

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
5.

A mass spectrometry proteomics data management platform.

Sharma V, Eng JK, Maccoss MJ, Riffle M.

Mol Cell Proteomics. 2012 Sep;11(9):824-31. doi: 10.1074/mcp.O111.015149. Epub 2012 May 18.

6.

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.

PMID:
26182917
7.

The OMSSAPercolator: an automated tool to validate OMSSA results.

Wen B, Li G, Wright JC, Du C, Feng Q, Xu X, Choudhary JS, Wang J.

Proteomics. 2014 May;14(9):1011-4. doi: 10.1002/pmic.201300393. Epub 2014 Mar 12.

PMID:
24504981
8.

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
9.

ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry.

Brusniak MY, Kwok ST, Christiansen M, Campbell D, Reiter L, Picotti P, Kusebauch U, Ramos H, Deutsch EW, Chen J, Moritz RL, Aebersold R.

BMC Bioinformatics. 2011 Mar 18;12:78. doi: 10.1186/1471-2105-12-78.

10.

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.

11.

Bioinformatics in mass spectrometry data analysis for proteomics studies.

Cristoni S, Bernardi LR.

Expert Rev Proteomics. 2004 Dec;1(4):469-83. Review.

PMID:
15966842
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.

Mascot file parsing and quantification (MFPaQ), a new software to parse, validate, and quantify proteomics data generated by ICAT and SILAC mass spectrometric analyses: application to the proteomics study of membrane proteins from primary human endothelial cells.

Bouyssié D, Gonzalez de Peredo A, Mouton E, Albigot R, Roussel L, Ortega N, Cayrol C, Burlet-Schiltz O, Girard JP, Monsarrat B.

Mol Cell Proteomics. 2007 Sep;6(9):1621-37. Epub 2007 May 28.

14.

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.

15.

The amino acid's backup bone - storage solutions for proteomics facilities.

Meckel H, Stephan C, Bunse C, Krafzik M, Reher C, Kohl M, Meyer HE, Eisenacher M.

Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):2-11. doi: 10.1016/j.bbapap.2013.05.018. Epub 2013 May 27.

16.

SRMBuilder: a user-friendly tool for selected reaction monitoring data analysis.

Sheng Q, Wu C, Su Z, Zeng R.

J Bioinform Comput Biol. 2011 Dec;9 Suppl 1:51-62.

PMID:
22144253
17.

2DDB - a bioinformatics solution for analysis of quantitative proteomics data.

Malmström L, Marko-Varga G, Westergren-Thorsson G, Laurell T, Malmström J.

BMC Bioinformatics. 2006 Mar 20;7:158.

18.

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.

19.

multiplierz: an extensible API based desktop environment for proteomics data analysis.

Parikh JR, Askenazi M, Ficarro SB, Cashorali T, Webber JT, Blank NC, Zhang Y, Marto JA.

BMC Bioinformatics. 2009 Oct 29;10:364. doi: 10.1186/1471-2105-10-364.

20.

Analysis of mass spectrometry data in proteomics.

Matthiesen R, Jensen ON.

Methods Mol Biol. 2008;453:105-22. doi: 10.1007/978-1-60327-429-6_4.

PMID:
18712299

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