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Items: 1 to 20 of 103


Basophile: accurate fragment charge state prediction improves peptide identification rates.

Wang D, Dasari S, Chambers MC, Holman JD, Chen K, Liebler DC, Orton DJ, Purvine SO, Monroe ME, Chung CY, Rose KL, Tabb DL.

Genomics Proteomics Bioinformatics. 2013 Apr;11(2):86-95. doi: 10.1016/j.gpb.2012.11.004. Epub 2013 Mar 8.


pNovo: de novo peptide sequencing and identification using HCD spectra.

Chi H, Sun RX, Yang B, Song CQ, Wang LH, Liu C, Fu Y, Yuan ZF, Wang HP, He SM, Dong MQ.

J Proteome Res. 2010 May 7;9(5):2713-24. doi: 10.1021/pr100182k.


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.


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.


Statistical characterization of HCD fragmentation patterns of tryptic peptides on an LTQ Orbitrap Velos mass spectrometer.

Shao C, Zhang Y, Sun W.

J Proteomics. 2014 Sep 23;109:26-37. doi: 10.1016/j.jprot.2014.06.012. Epub 2014 Jun 27.


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.


Effectiveness of CID, HCD, and ETD with FT MS/MS for degradomic-peptidomic analysis: comparison of peptide identification methods.

Shen Y, Tolić N, Xie F, Zhao R, Purvine SO, Schepmoes AA, Moore RJ, Anderson GA, Smith RD.

J Proteome Res. 2011 Sep 2;10(9):3929-43. doi: 10.1021/pr200052c. Epub 2011 Aug 15.


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.


MS-Simulator: predicting y-ion intensities for peptides with two charges based on the intensity ratio of neighboring ions.

Sun S, Yang F, Yang Q, Zhang H, Wang Y, Bu D, Ma B.

J Proteome Res. 2012 Sep 7;11(9):4509-16. doi: 10.1021/pr300235v. Epub 2012 Jul 31.


Occurrence of C-terminal residue exclusion in peptide fragmentation by ESI and MALDI tandem mass spectrometry.

Dupré M, Cantel S, Martinez J, Enjalbal C.

J Am Soc Mass Spectrom. 2012 Feb;23(2):330-46. doi: 10.1007/s13361-011-0254-1. Epub 2011 Nov 18.


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.


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.


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.


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

Zhang Z.

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


Predicting intensity ranks of peptide fragment ions.

Frank AM.

J Proteome Res. 2009 May;8(5):2226-40. doi: 10.1021/pr800677f.


Analytical utility of mass spectral binning in proteomic experiments by SPectral Immonium Ion Detection (SPIID).

Kelstrup CD, Frese C, Heck AJ, Olsen JV, Nielsen ML.

Mol Cell Proteomics. 2014 Aug;13(8):1914-24. doi: 10.1074/mcp.O113.035915. Epub 2014 Jun 3.


Precursor charge state prediction for electron transfer dissociation tandem mass spectra.

Sharma V, Eng JK, Feldman S, von Haller PD, MacCoss MJ, Noble WS.

J Proteome Res. 2010 Oct 1;9(10):5438-44. doi: 10.1021/pr1006685.


Calculations of relative intensities of fragment ions in the MSMS spectra of a doubly charged penta-peptide.

Pechan T, Gwaltney SR.

BMC Bioinformatics. 2012;13 Suppl 15:S13. doi: 10.1186/1471-2105-13-S15-S13. Epub 2012 Sep 11.


MAZIE: a mass and charge inference engine to enhance database searching of tandem mass spectra.

Victor KG, Murgai M, Lyons CE, Templeton TA, Moshnikov SA, Templeton DJ.

J Am Soc Mass Spectrom. 2010 Jan;21(1):80-7. doi: 10.1016/j.jasms.2009.09.007. Epub 2009 Sep 17.


Improved peptide identification by targeted fragmentation using CID, HCD and ETD on an LTQ-Orbitrap Velos.

Frese CK, Altelaar AF, Hennrich ML, Nolting D, Zeller M, Griep-Raming J, Heck AJ, Mohammed S.

J Proteome Res. 2011 May 6;10(5):2377-88. doi: 10.1021/pr1011729. Epub 2011 Apr 1.

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