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Items: 1 to 20 of 134

1.

HTAPP: high-throughput autonomous proteomic pipeline.

Yu K, Salomon AR.

Proteomics. 2010 Jun;10(11):2113-22. doi: 10.1002/pmic.200900159.

2.
3.

Integrated platform for manual and high-throughput statistical validation of tandem mass spectra.

Yu K, Sabelli A, DeKeukelaere L, Park R, Sindi S, Gatsonis CA, Salomon A.

Proteomics. 2009 Jun;9(11):3115-25. doi: 10.1002/pmic.200800899.

4.

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.

5.

Benchmarking quantitative label-free LC-MS data processing workflows using a complex spiked proteomic standard dataset.

Ramus C, Hovasse A, Marcellin M, Hesse AM, Mouton-Barbosa E, Bouyssié D, Vaca S, Carapito C, Chaoui K, Bruley C, Garin J, Cianférani S, Ferro M, Van Dorssaeler A, Burlet-Schiltz O, Schaeffer C, Couté Y, Gonzalez de Peredo A.

J Proteomics. 2016 Jan 30;132:51-62. doi: 10.1016/j.jprot.2015.11.011.

PMID:
26585461
6.

Translational Metabolomics of Head Injury: Exploring Dysfunctional Cerebral Metabolism with Ex Vivo NMR Spectroscopy-Based Metabolite Quantification.

Wolahan SM, Hirt D, Glenn TC.

In: Kobeissy FH, editor. Brain Neurotrauma: Molecular, Neuropsychological, and Rehabilitation Aspects. Boca Raton (FL): CRC Press/Taylor & Francis; 2015. Chapter 25.

7.

Abacus: a computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis.

Fermin D, Basrur V, Yocum AK, Nesvizhskii AI.

Proteomics. 2011 Apr;11(7):1340-5. doi: 10.1002/pmic.201000650.

8.

Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline.

Slagel J, Mendoza L, Shteynberg D, Deutsch EW, Moritz RL.

Mol Cell Proteomics. 2015 Feb;14(2):399-404. doi: 10.1074/mcp.O114.043380.

9.

Trans-proteomic pipeline: a pipeline for proteomic analysis.

Pedrioli PG.

Methods Mol Biol. 2010;604:213-38. doi: 10.1007/978-1-60761-444-9_15.

PMID:
20013374
10.

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.

11.

A guided tour of the Trans-Proteomic Pipeline.

Deutsch EW, Mendoza L, Shteynberg D, Farrah T, Lam H, Tasman N, Sun Z, Nilsson E, Pratt B, Prazen B, Eng JK, Martin DB, Nesvizhskii AI, Aebersold R.

Proteomics. 2010 Mar;10(6):1150-9. doi: 10.1002/pmic.200900375. Review.

12.

Methods for visual mining of genomic and proteomic data atlases.

Boyle J, Kreisberg R, Bressler R, Killcoyne S.

BMC Bioinformatics. 2012 Apr 23;13:58. doi: 10.1186/1471-2105-13-58.

14.

An automated pipeline for high-throughput label-free quantitative proteomics.

Weisser H, Nahnsen S, Grossmann J, Nilse L, Quandt A, Brauer H, Sturm M, Kenar E, Kohlbacher O, Aebersold R, Malmström L.

J Proteome Res. 2013 Apr 5;12(4):1628-44. doi: 10.1021/pr300992u.

PMID:
23391308
15.

A streamlined approach to high-throughput proteomics.

Stephens AN, Quach P, Harry EJ.

Expert Rev Proteomics. 2005 Apr;2(2):173-85. Review.

PMID:
15892563
16.

APP: an Automated Proteomics Pipeline for the analysis of mass spectrometry data based on multiple open access tools.

Malm EK, Srivastava V, Sundqvist G, Bulone V.

BMC Bioinformatics. 2014 Dec 30;15:441. doi: 10.1186/s12859-014-0441-8.

17.

CHOMPER: a bioinformatic tool for rapid validation of tandem mass spectrometry search results associated with high-throughput proteomic strategies.

Eddes JS, Kapp EA, Frecklington DF, Connolly LM, Layton MJ, Moritz RL, Simpson RJ.

Proteomics. 2002 Sep;2(9):1097-103.

PMID:
12362328
18.

TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data.

Junker J, Bielow C, Bertsch A, Sturm M, Reinert K, Kohlbacher O.

J Proteome Res. 2012 Jul 6;11(7):3914-20. doi: 10.1021/pr300187f.

PMID:
22583024
19.

Development and validation of a spectral library searching method for peptide identification from MS/MS.

Lam H, Deutsch EW, Eddes JS, Eng JK, King N, Stein SE, Aebersold R.

Proteomics. 2007 Mar;7(5):655-67.

PMID:
17295354
20.

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data.

Peterson ES, McCue LA, Schrimpe-Rutledge AC, Jensen JL, Walker H, Kobold MA, Webb SR, Payne SH, Ansong C, Adkins JN, Cannon WR, Webb-Robertson BJ.

BMC Genomics. 2012 Apr 5;13:131. doi: 10.1186/1471-2164-13-131.

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