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Items: 1 to 20 of 92

1.

On the accuracy and limits of peptide fragmentation spectrum prediction.

Li S, Arnold RJ, Tang H, Radivojac P.

Anal Chem. 2011 Feb 1;83(3):790-6. doi: 10.1021/ac102272r. Epub 2010 Dec 22.

2.

A simulated MS/MS library for spectrum-to-spectrum searching in large scale identification of proteins.

Yen CY, Meyer-Arendt K, Eichelberger B, Sun S, Houel S, Old WM, Knight R, Ahn NG, Hunter LE, Resing KA.

Mol Cell Proteomics. 2009 Apr;8(4):857-69. doi: 10.1074/mcp.M800384-MCP200. Epub 2008 Dec 22.

3.

Extending the coverage of spectral libraries: a neighbor-based approach to predicting intensities of peptide fragmentation spectra.

Ji C, Arnold RJ, Sokoloski KJ, Hardy RW, Tang H, Radivojac P.

Proteomics. 2013 Mar;13(5):756-65. doi: 10.1002/pmic.201100670. Epub 2013 Feb 4.

4.

Spectrum-to-spectrum searching using a proteome-wide spectral library.

Yen CY, Houel S, Ahn NG, Old WM.

Mol Cell Proteomics. 2011 Jul;10(7):M111.007666. doi: 10.1074/mcp.M111.007666. Epub 2011 Apr 30.

5.

Prediction of low-energy collision-induced dissociation spectra of peptides.

Zhang Z.

Anal Chem. 2004 Jul 15;76(14):3908-22.

PMID:
15253624
6.

Identification of proteins and phosphoproteins using pulsed Q collision induced dissociation (PQD).

Wu WW, Wang G, Insel PA, Hsiao CT, Zou S, Maudsley S, Martin B, Shen RF.

J Am Soc Mass Spectrom. 2011 Oct;22(10):1753-62. doi: 10.1007/s13361-011-0197-6. Epub 2011 Jul 15.

7.

OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction.

Wang Y, Yang F, Wu P, Bu D, Sun S.

BMC Bioinformatics. 2015 Apr 2;16:110. doi: 10.1186/s12859-015-0540-1.

9.

A machine learning approach to predicting peptide fragmentation spectra.

Arnold RJ, Jayasankar N, Aggarwal D, Tang H, Radivojac P.

Pac Symp Biocomput. 2006:219-30.

10.

Improved peptide identification for proteomic analysis based on comprehensive characterization of electron transfer dissociation spectra.

Sun RX, Dong MQ, Song CQ, Chi H, Yang B, Xiu LY, Tao L, Jing ZY, Liu C, Wang LH, Fu Y, He SM.

J Proteome Res. 2010 Dec 3;9(12):6354-67. doi: 10.1021/pr100648r. Epub 2010 Nov 12.

PMID:
20883037
11.

Improved validation of peptide MS/MS assignments using spectral intensity prediction.

Sun S, Meyer-Arendt K, Eichelberger B, Brown R, Yen CY, Old WM, Pierce K, Cios KJ, Ahn NG, Resing KA.

Mol Cell Proteomics. 2007 Jan;6(1):1-17. Epub 2006 Oct 2.

12.

Prediction of peptide fragment ion mass spectra by data mining techniques.

Dong NP, Liang YZ, Xu QS, Mok DK, Yi LZ, Lu HM, He M, Fan W.

Anal Chem. 2014 Aug 5;86(15):7446-54. doi: 10.1021/ac501094m. Epub 2014 Jul 25.

PMID:
25032905
13.

Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation.

Olsen JV, Mann M.

Proc Natl Acad Sci U S A. 2004 Sep 14;101(37):13417-22. Epub 2004 Sep 3.

14.

Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility.

Tabb DL, MacCoss MJ, Wu CC, Anderson SD, Yates JR 3rd.

Anal Chem. 2003 May 15;75(10):2470-7.

PMID:
12918992
15.

Improving SRM assay development: a global comparison between triple quadrupole, ion trap, and higher energy CID peptide fragmentation spectra.

de Graaf EL, Altelaar AF, van Breukelen B, Mohammed S, Heck AJ.

J Proteome Res. 2011 Sep 2;10(9):4334-41. doi: 10.1021/pr200156b. Epub 2011 Jul 21.

PMID:
21726076
16.

Effects of electron-transfer coupled with collision-induced dissociation (ET/CID) on doubly charged peptides and phosphopeptides.

Liu CW, Lai CC.

J Am Soc Mass Spectrom. 2011 Jan;22(1):57-66. doi: 10.1007/s13361-010-0020-9. Epub 2011 Jan 27.

PMID:
21472544
17.

Code developments to improve the efficiency of automated MS/MS spectra interpretation.

Sadygov RG, Eng J, Durr E, Saraf A, McDonald H, MacCoss MJ, Yates JR 3rd.

J Proteome Res. 2002 May-Jun;1(3):211-5.

PMID:
12645897
18.

Identification of related peptides through the analysis of fragment ion mass shifts.

Wilhelm T, Jones AM.

J Proteome Res. 2014 Sep 5;13(9):4002-11. doi: 10.1021/pr500347e. Epub 2014 Aug 5.

PMID:
25058668
19.

The utility of accurate mass and LC elution time information in the analysis of complex proteomes.

Norbeck AD, Monroe ME, Adkins JN, Anderson KK, Daly DS, Smith RD.

J Am Soc Mass Spectrom. 2005 Aug;16(8):1239-49.

20.

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.

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