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Similar articles for PubMed (Select 22052992)

1.

Direct maximization of protein identifications from tandem mass spectra.

Spivak M, Weston J, Tomazela D, MacCoss MJ, Noble WS.

Mol Cell Proteomics. 2012 Feb;11(2):M111.012161. doi: 10.1074/mcp.M111.012161. Epub 2011 Nov 3.

2.

Semi-supervised learning for peptide identification from shotgun proteomics datasets.

Käll L, Canterbury JD, Weston J, Noble WS, MacCoss MJ.

Nat Methods. 2007 Nov;4(11):923-5. Epub 2007 Oct 21.

PMID:
17952086
3.
4.

Learning score function parameters for improved spectrum identification in tandem mass spectrometry experiments.

Spivak M, Bereman MS, Maccoss MJ, Noble WS.

J Proteome Res. 2012 Sep 7;11(9):4499-508. doi: 10.1021/pr300234m. Epub 2012 Aug 15.

5.

Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics.

Choi H, Nesvizhskii AI.

J Proteome Res. 2008 Jan;7(1):254-65. Epub 2007 Dec 27.

PMID:
18159924
6.

Enhanced peptide identification by electron transfer dissociation using an improved Mascot Percolator.

Wright JC, Collins MO, Yu L, Käll L, Brosch M, Choudhary JS.

Mol Cell Proteomics. 2012 Aug;11(8):478-91. doi: 10.1074/mcp.O111.014522. Epub 2012 Apr 6.

7.

IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering.

Ma ZQ, Dasari S, Chambers MC, Litton MD, Sobecki SM, Zimmerman LJ, Halvey PJ, Schilling B, Drake PM, Gibson BW, Tabb DL.

J Proteome Res. 2009 Aug;8(8):3872-81. doi: 10.1021/pr900360j.

8.

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.

9.

PatternLab for proteomics: a tool for differential shotgun proteomics.

Carvalho PC, Fischer JS, Chen EI, Yates JR 3rd, Barbosa VC.

BMC Bioinformatics. 2008 Jul 21;9:316. doi: 10.1186/1471-2105-9-316.

10.

MUMAL: multivariate analysis in shotgun proteomics using machine learning techniques.

Cerqueira FR, Ferreira RS, Oliveira AP, Gomes AP, Ramos HJ, Graber A, Baumgartner C.

BMC Genomics. 2012;13 Suppl 5:S4. doi: 10.1186/1471-2164-13-S5-S4. Epub 2012 Oct 19.

11.

Shotgun protein identification and quantification by mass spectrometry.

Lu B, Xu T, Park SK, Yates JR 3rd.

Methods Mol Biol. 2009;564:261-88. doi: 10.1007/978-1-60761-157-8_15.

PMID:
19544028
12.

Peptide identification by database search of mixture tandem mass spectra.

Wang J, Bourne PE, Bandeira N.

Mol Cell Proteomics. 2011 Dec;10(12):M111.010017. doi: 10.1074/mcp.M111.010017. Epub 2011 Aug 23.

13.

RT-SVR+q: a strategy for post-Mascot analysis using retention time and q value metric to improve peptide and protein identifications.

Cao W, Ma D, Kapur A, Patankar MS, Ma Y, Li L.

J Proteomics. 2011 Dec 21;75(2):480-90. doi: 10.1016/j.jprot.2011.08.013. Epub 2011 Aug 24.

14.

Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra.

Venable JD, Dong MQ, Wohlschlegel J, Dillin A, Yates JR.

Nat Methods. 2004 Oct;1(1):39-45. Epub 2004 Sep 29.

PMID:
15782151
15.

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.

16.

False discovery rates and related statistical concepts in mass spectrometry-based proteomics.

Choi H, Nesvizhskii AI.

J Proteome Res. 2008 Jan;7(1):47-50. Epub 2007 Dec 8.

PMID:
18067251
17.

Oscore: a combined score to reduce false negative rates for peptide identification in tandem mass spectrometry analysis.

Shao C, Sun W, Li F, Yang R, Zhang L, Gao Y.

J Mass Spectrom. 2009 Jan;44(1):25-31. doi: 10.1002/jms.1466.

PMID:
18698557
18.

A proteomics search algorithm specifically designed for high-resolution tandem mass spectra.

Wenger CD, Coon JJ.

J Proteome Res. 2013 Mar 1;12(3):1377-86. doi: 10.1021/pr301024c. Epub 2013 Jan 31.

19.

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.

20.

Protein identification by tandem mass spectrometry and sequence database searching.

Nesvizhskii AI.

Methods Mol Biol. 2007;367:87-119. Review.

PMID:
17185772
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