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Items: 1 to 20 of 68

1.

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.

2.

Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry.

Reiter L, Claassen M, Schrimpf SP, Jovanovic M, Schmidt A, Buhmann JM, Hengartner MO, Aebersold R.

Mol Cell Proteomics. 2009 Nov;8(11):2405-17. doi: 10.1074/mcp.M900317-MCP200. Epub 2009 Jul 16.

3.

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
4.

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.

5.

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.

6.

False discovery rates of protein identifications: a strike against the two-peptide rule.

Gupta N, Pevzner PA.

J Proteome Res. 2009 Sep;8(9):4173-81. doi: 10.1021/pr9004794.

7.

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
8.

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
9.

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
10.

Added value for tandem mass spectrometry shotgun proteomics data validation through isoelectric focusing of peptides.

Heller M, Ye M, Michel PE, Morier P, Stalder D, Jünger MA, Aebersold R, Reymond F, Rossier JS.

J Proteome Res. 2005 Nov-Dec;4(6):2273-82.

PMID:
16335976
11.

Practical and Efficient Searching in Proteomics: A Cross Engine Comparison.

Paulo JA.

Webmedcentral. 2013 Oct 1;4(10). pii: WMCPLS0052.

12.

Comparative shotgun proteomics using spectral count data and quasi-likelihood modeling.

Li M, Gray W, Zhang H, Chung CH, Billheimer D, Yarbrough WG, Liebler DC, Shyr Y, Slebos RJ.

J Proteome Res. 2010 Aug 6;9(8):4295-305. doi: 10.1021/pr100527g. Erratum in: J Proteome Res. 2010 Nov 5;9(11):6090.

13.

PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface.

Uszkoreit J, Maerkens A, Perez-Riverol Y, Meyer HE, Marcus K, Stephan C, Kohlbacher O, Eisenacher M.

J Proteome Res. 2015 Jul 2;14(7):2988-97. doi: 10.1021/acs.jproteome.5b00121. Epub 2015 Jun 10.

PMID:
25938255
14.

Analysis of high accuracy, quantitative proteomics data in the MaxQB database.

Schaab C, Geiger T, Stoehr G, Cox J, Mann M.

Mol Cell Proteomics. 2012 Mar;11(3):M111.014068. doi: 10.1074/mcp.M111.014068. Epub 2012 Feb 2.

15.

Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data.

Serang O, MacCoss MJ, Noble WS.

J Proteome Res. 2010 Oct 1;9(10):5346-57. doi: 10.1021/pr100594k.

16.

Protein inference: a review.

Huang T, Wang J, Yu W, He Z.

Brief Bioinform. 2012 Sep;13(5):586-614. doi: 10.1093/bib/bbs004. Epub 2012 Feb 28. Review.

17.

Database search strategies for proteomic data sets generated by electron capture dissociation mass spectrometry.

Sweet SM, Jones AW, Cunningham DL, Heath JK, Creese AJ, Cooper HJ.

J Proteome Res. 2009 Dec;8(12):5475-84. doi: 10.1021/pr9008282.

18.

Proteomics in Caenorhabditis elegans.

Audhya A, Desai A.

Brief Funct Genomic Proteomic. 2008 May;7(3):205-10. doi: 10.1093/bfgp/eln014. Epub 2008 Mar 27. Review.

19.

Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases.

Kim S, Gupta N, Pevzner PA.

J Proteome Res. 2008 Aug;7(8):3354-63. doi: 10.1021/pr8001244. Epub 2008 Jul 3.

20.

Using the PRIDE proteomics identifications database for knowledge discovery and data analysis.

Jones P, Martens L.

Methods Mol Biol. 2010;604:297-307. doi: 10.1007/978-1-60761-444-9_20.

PMID:
20013379
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