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Results: 1 to 20 of 101

1.

Combining results of multiple search engines in proteomics.

Shteynberg D, Nesvizhskii AI, Moritz RL, Deutsch EW.

Mol Cell Proteomics. 2013 Sep;12(9):2383-93. doi: 10.1074/mcp.R113.027797. Epub 2013 May 29. Review.

PMID:
23720762
[PubMed - indexed for MEDLINE]
2.

MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines.

Kwon T, Choi H, Vogel C, Nesvizhskii AI, Marcotte EM.

J Proteome Res. 2011 Jul 1;10(7):2949-58. doi: 10.1021/pr2002116. Epub 2011 Apr 29.

PMID:
21488652
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
19253293
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Quality assessments of peptide-spectrum matches in shotgun proteomics.

Granholm V, Käll L.

Proteomics. 2011 Mar;11(6):1086-93. doi: 10.1002/pmic.201000432. Epub 2011 Feb 7.

PMID:
21365749
[PubMed - indexed for MEDLINE]
5.

Maximizing the sensitivity and reliability of peptide identification in large-scale proteomic experiments by harnessing multiple search engines.

Yu W, Taylor JA, Davis MT, Bonilla LE, Lee KA, Auger PL, Farnsworth CC, Welcher AA, Patterson SD.

Proteomics. 2010 Mar;10(6):1172-89. doi: 10.1002/pmic.200900074.

PMID:
20101609
[PubMed - indexed for MEDLINE]
6.

iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates.

Shteynberg D, Deutsch EW, Lam H, Eng JK, Sun Z, Tasman N, Mendoza L, Moritz RL, Aebersold R, Nesvizhskii AI.

Mol Cell Proteomics. 2011 Dec;10(12):M111.007690. doi: 10.1074/mcp.M111.007690. Epub 2011 Aug 29.

PMID:
21876204
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Algorithms for database-dependent search of MS/MS data.

Matthiesen R.

Methods Mol Biol. 2013;1007:119-38. doi: 10.1007/978-1-62703-392-3_5.

PMID:
23666724
[PubMed - indexed for MEDLINE]
8.

Estimating the statistical significance of peptide identifications from shotgun proteomics experiments.

Higgs RE, Knierman MD, Freeman AB, Gelbert LM, Patil ST, Hale JE.

J Proteome Res. 2007 May;6(5):1758-67. Epub 2007 Mar 31.

PMID:
17397207
[PubMed - indexed for MEDLINE]
9.

Search and decoy: the automatic identification of mass spectra.

Eisenacher M, Kohl M, Turewicz M, Koch MH, Uszkoreit J, Stephan C.

Methods Mol Biol. 2012;893:445-88. doi: 10.1007/978-1-61779-885-6_28.

PMID:
22665317
[PubMed - indexed for MEDLINE]
10.

BuildSummary: using a group-based approach to improve the sensitivity of peptide/protein identification in shotgun proteomics.

Sheng Q, Dai J, Wu Y, Tang H, Zeng R.

J Proteome Res. 2012 Mar 2;11(3):1494-502. doi: 10.1021/pr200194p. Epub 2012 Feb 8.

PMID:
22217156
[PubMed - indexed for MEDLINE]
11.

Refining comparative proteomics by spectral counting to account for shared peptides and multiple search engines.

Chen YY, Dasari S, Ma ZQ, Vega-Montoto LJ, Li M, Tabb DL.

Anal Bioanal Chem. 2012 Sep;404(4):1115-25. doi: 10.1007/s00216-012-6011-x. Epub 2012 May 3.

PMID:
22552787
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis.

Tabb DL, Fernando CG, Chambers MC.

J Proteome Res. 2007 Feb;6(2):654-61.

PMID:
17269722
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Andromeda: a peptide search engine integrated into the MaxQuant environment.

Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M.

J Proteome Res. 2011 Apr 1;10(4):1794-805. doi: 10.1021/pr101065j. Epub 2011 Feb 22.

PMID:
21254760
[PubMed - indexed for MEDLINE]
14.

Generic comparison of protein inference engines.

Claassen M, Reiter L, Hengartner MO, Buhmann JM, Aebersold R.

Mol Cell Proteomics. 2012 Apr;11(4):O110.007088. doi: 10.1074/mcp.O110.007088. Epub 2011 Nov 4.

PMID:
22057310
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
21222473
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

High-throughput database search and large-scale negative polarity liquid chromatography-tandem mass spectrometry with ultraviolet photodissociation for complex proteomic samples.

Madsen JA, Xu H, Robinson MR, Horton AP, Shaw JB, Giles DK, Kaoud TS, Dalby KN, Trent MS, Brodbelt JS.

Mol Cell Proteomics. 2013 Sep;12(9):2604-14. doi: 10.1074/mcp.O113.028258. Epub 2013 May 21.

PMID:
23695934
[PubMed - indexed for MEDLINE]
17.

Data maximization by multipass analysis of protein mass spectra.

Tharakan R, Edwards N, Graham DR.

Proteomics. 2010 Mar;10(6):1160-71. doi: 10.1002/pmic.200900433. Review.

PMID:
20082346
[PubMed - indexed for MEDLINE]
18.

Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies.

Searle BC, Turner M, Nesvizhskii AI.

J Proteome Res. 2008 Jan;7(1):245-53. doi: 10.1021/pr070540w.

PMID:
18173222
[PubMed - indexed for MEDLINE]
19.

A novel algorithm for validating peptide identification from a shotgun proteomics search engine.

Jian L, Niu X, Xia Z, Samir P, Sumanasekera C, Mu Z, Jennings JL, Hoek KL, Allos T, Howard LM, Edwards KM, Weil PA, Link AJ.

J Proteome Res. 2013 Mar 1;12(3):1108-19. doi: 10.1021/pr300631t. Epub 2013 Feb 12.

PMID:
23402659
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

General framework for developing and evaluating database scoring algorithms using the TANDEM search engine.

MacLean B, Eng JK, Beavis RC, McIntosh M.

Bioinformatics. 2006 Nov 15;22(22):2830-2. Epub 2006 Jul 28.

PMID:
16877754
[PubMed - indexed for MEDLINE]
Free Article

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