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Items: 1 to 20 of 206


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.


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.


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.


The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search.

Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, Mohammed S, Heck AJ, Pevzner PA.

Mol Cell Proteomics. 2010 Dec;9(12):2840-52. doi: 10.1074/mcp.M110.003731. Epub 2010 Sep 9.


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.


Optimization of Search Engines and Postprocessing Approaches to Maximize Peptide and Protein Identification for High-Resolution Mass Data.

Tu C, Sheng Q, Li J, Ma D, Shen X, Wang X, Shyr Y, Yi Z, Qu J.

J Proteome Res. 2015 Nov 6;14(11):4662-73. doi: 10.1021/acs.jproteome.5b00536. Epub 2015 Sep 30.


De novo peptide sequencing using CID and HCD spectra pairs.

Yan Y, Kusalik AJ, Wu FX.

Proteomics. 2016 Oct;16(20):2615-2624. doi: 10.1002/pmic.201500251. Epub 2016 Aug 24.


Better score function for peptide identification with ETD MS/MS spectra.

Liu X, Shan B, Xin L, Ma B.

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S4. doi: 10.1186/1471-2105-11-S1-S4.


Comparison of data analysis parameters and MS/MS fragmentation techniques for quantitative proteome analysis using isobaric peptide termini labeling (IPTL).

Koehler CJ, Arntzen MØ, Treumann A, Thiede B.

Anal Bioanal Chem. 2012 Sep;404(4):1103-14. doi: 10.1007/s00216-012-5949-z. Epub 2012 Mar 31.


Proteome analysis of Sorangium cellulosum employing 2D-HPLC-MS/MS and improved database searching strategies for CID and ETD fragment spectra.

Leinenbach A, Hartmer R, Lubeck M, Kneissl B, Elnakady YA, Baessmann C, Müller R, Huber CG.

J Proteome Res. 2009 Sep;8(9):4350-61. doi: 10.1021/pr9004647.


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.


Mass spectrometric de novo sequencing of natural non-tryptic peptides: comparing peculiarities of collision-induced dissociation (CID) and high energy collision dissociation (HCD).

Samgina TY, Vorontsov EA, Gorshkov VA, Artemenko KA, Zubarev RA, Lebedev AT.

Rapid Commun Mass Spectrom. 2014 Dec 15;28(23):2595-604. doi: 10.1002/rcm.7049.


Combining low- and high-energy tandem mass spectra for optimized peptide quantification with isobaric tags.

Dayon L, Pasquarello C, Hoogland C, Sanchez JC, Scherl A.

J Proteomics. 2010 Feb 10;73(4):769-77. doi: 10.1016/j.jprot.2009.10.015. Epub 2009 Nov 10.


Comparison of higher energy collisional dissociation and collision-induced dissociation MS/MS sequencing methods for identification of naturally occurring peptides in human urine.

Pejchinovski M, Klein J, Ramírez-Torres A, Bitsika V, Mermelekas G, Vlahou A, Mullen W, Mischak H, Jankowski V.

Proteomics Clin Appl. 2015 Jun;9(5-6):531-42. doi: 10.1002/prca.201400163.


Large-scale identification of endogenous secretory peptides using electron transfer dissociation mass spectrometry.

Sasaki K, Osaki T, Minamino N.

Mol Cell Proteomics. 2013 Mar;12(3):700-9. doi: 10.1074/mcp.M112.017400. Epub 2012 Dec 18.


Characteristic tandem mass spectral features under various collision chemistries for site-specific identification of protein S-glutathionylation.

Chou CC, Chiang BY, Lin JC, Pan KT, Lin CH, Khoo KH.

J Am Soc Mass Spectrom. 2015 Jan;26(1):120-32. doi: 10.1007/s13361-014-1014-9. Epub 2014 Nov 6.


MS Amanda, a universal identification algorithm optimized for high accuracy tandem mass spectra.

Dorfer V, Pichler P, Stranzl T, Stadlmann J, Taus T, Winkler S, Mechtler K.

J Proteome Res. 2014 Aug 1;13(8):3679-84. doi: 10.1021/pr500202e. Epub 2014 Jun 26.


Sequencing-grade de novo analysis of MS/MS triplets (CID/HCD/ETD) from overlapping peptides.

Guthals A, Clauser KR, Frank AM, Bandeira N.

J Proteome Res. 2013 Jun 7;12(6):2846-57. doi: 10.1021/pr400173d. Epub 2013 May 30.

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