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

[1]  Tibor Pechan,et al.  Calculations of relative intensities of fragment ions in the MSMS spectra of a doubly charged penta-peptide , 2012, BMC Bioinformatics.

[2]  Zhongqi Zhang Prediction of collision-induced-dissociation spectra of peptides with post-translational or process-induced modifications. , 2011, Analytical chemistry.

[3]  K. Siu,et al.  Doubly charged protonated a ions derived from small peptides. , 2011, Physical chemistry chemical physics : PCCP.

[4]  Rajeev Kumar Sinha,et al.  Diagnosing the Protonation Site of b2 Peptide Fragment Ions using IRMPD in the X–H (X = O, N, and C) Stretching Region , 2011, Journal of the American Society for Mass Spectrometry.

[5]  Douglas J. Baxter,et al.  Large improvements in MS/MS-based peptide identification rates using a hybrid analysis. , 2011, Journal of proteome research.

[6]  S. Suhai,et al.  Towards Understanding the Tandem Mass Spectra of Protonated Oligopeptides. 2: The Proline Effect in Collision-Induced Dissociation of Protonated Ala-Ala-Xxx-Pro-Ala (Xxx = Ala, Ser, Leu, Val, Phe, and Trp) , 2011, Journal of the American Society for Mass Spectrometry.

[7]  A. G. Harrison Effect of the Identity of Xaa on the Fragmentation Modes of Doubly-Protonated Ala-Ala-Xaa-Ala-Ala-Ala-Arg , 2011, Journal of the American Society for Mass Spectrometry.

[8]  D. S. Richards,et al.  Kinetic Control of Protonation in Electrospray Ionization , 2011, Journal of the American Society for Mass Spectrometry.

[9]  Zhongqi Zhang,et al.  Prediction of collision-induced dissociation spectra of common N-glycopeptides for glycoform identification. , 2010, Analytical chemistry.

[10]  B. Paizs,et al.  Effect of the his residue on the cyclization of b ions , 2010, Journal of the American Society for Mass Spectrometry.

[11]  Ryan P. Dain,et al.  Structure of [M + H - H(2)O](+) from protonated tetraglycine revealed by tandem mass spectrometry and IRMPD spectroscopy. , 2010, The journal of physical chemistry. A.

[12]  Zhongqi Zhang,et al.  Prediction of electron-transfer/capture dissociation spectra of peptides. , 2010, Analytical chemistry.

[13]  B. Paizs,et al.  Fragmentation of doubly-protonated Pro-His-Xaa tripeptides: Formation of b22+ ions , 2009, Journal of the American Society for Mass Spectrometry.

[14]  Ari Frank,et al.  Predicting intensity ranks of peptide fragment ions. , 2009, Journal of proteome research.

[15]  B. Paizs,et al.  What is the structure of b2 ions generated from doubly protonated tryptic peptides? , 2009, Journal of the American Society for Mass Spectrometry.

[16]  S. Suhai,et al.  Sequence-scrambling fragmentation pathways of protonated peptides. , 2008, Journal of the American Chemical Society.

[17]  Roman A. Zubarev,et al.  Bifurcating fragmentation behavior of gas-phase tryptic peptide dications in collisional activation , 2008, Journal of the American Society for Mass Spectrometry.

[18]  Jianfeng Feng,et al.  A machine learning approach to explore the spectra intensity pattern of peptides using tandem mass spectrometry data , 2008, BMC Bioinformatics.

[19]  Shawn T. Brown,et al.  Advances in methods and algorithms in a modern quantum chemistry program package. , 2006, Physical chemistry chemical physics : PCCP.

[20]  S. Gwaltney,et al.  Excitation Spectra of Dibenzoborole Containing π-Electron Systems: Controlling the Electronic Spectra by Changing the pπ−π* Conjugation , 2006 .

[21]  Zhongqi Zhang,et al.  Prediction of low-energy collision-induced dissociation spectra of peptides with three or more charges. , 2005, Analytical chemistry.

[22]  George C Tseng,et al.  Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns. , 2005, Analytical chemistry.

[23]  Sándor Suhai,et al.  Fragmentation pathways of protonated peptides. , 2005, Mass spectrometry reviews.

[24]  Robertson Craig,et al.  TANDEM: matching proteins with tandem mass spectra. , 2004, Bioinformatics.

[25]  S. Bryant,et al.  Open mass spectrometry search algorithm. , 2004, Journal of proteome research.

[26]  Zhongqi Zhang Prediction of low-energy collision-induced dissociation spectra of peptides. , 2004, Analytical chemistry.

[27]  Richard D. Smith,et al.  Dissociation behavior of doubly-charged tryptic peptides: correlation of gas-phase cleavage abundance with ramachandran plots. , 2004, Journal of the American Chemical Society.

[28]  A. Namane,et al.  Protein sequencing and identification using tandem mass spectrometry. Edited by Michael Kinter, Nicholas E. Sherman, published by Wiley-Interscience Series on Mass Spectrometry, 2000, 301 p. , 2002 .

[29]  S. Suhai,et al.  Combined quantum chemical and RRKM modeling of the main fragmentation pathways of protonated GGG. II. Formation of b(2), y(1), and y(2) ions. , 2002, Rapid communications in mass spectrometry : RCM.

[30]  S. Suhai,et al.  Proton mobility and main fragmentation pathways of protonated lysylglycine. , 2001, Rapid communications in mass spectrometry : RCM.

[31]  R. Aebersold,et al.  Mass spectrometry in proteomics. , 2001, Chemical reviews.

[32]  V. Wysocki,et al.  Mobile and localized protons: a framework for understanding peptide dissociation. , 2000, Journal of mass spectrometry : JMS.

[33]  N. Sherman,et al.  Protein Sequencing and Identification Using Tandem Mass Spectrometry: Kinter/Tandem Mass Spectrometry , 2000 .

[34]  D. N. Perkins,et al.  Probability‐based protein identification by searching sequence databases using mass spectrometry data , 1999, Electrophoresis.

[35]  Vicki H. Wysocki,et al.  Influence of Peptide Composition, Gas-Phase Basicity, and Chemical Modification on Fragmentation Efficiency: Evidence for the Mobile Proton Model , 1996 .

[36]  A Whiting,et al.  Role of the site of protonation in the low-energy decompositions of gas-phase peptide ions , 1996, Journal of the American Society for Mass Spectrometry.

[37]  J. Yates,et al.  An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database , 1994, Journal of the American Society for Mass Spectrometry.

[38]  R. Boyd,et al.  An investigation of fragmentation mechanisms of doubly protonated tryptic peptides. , 1992, Rapid communications in mass spectrometry : RCM.

[39]  Samuel P. Molesworth,et al.  Structure and Reactivity of a n and a n * Peptide Fragments Investigated Using Isotope Labeling, Tandem Mass Spectrometry, and Density Functional Theory Calculations* , 2011 .

[40]  Yan Zhao Intensity-based protein identification by machine learning from a library of tandem mass spectra , 2010 .

[41]  John C Whittaker,et al.  Review of factors that influence the abundance of ions produced in a tandem mass spectrometer and statistical methods for discovering these factors. , 2009, Mass spectrometry reviews.

[42]  S. Gwaltney,et al.  Excitation spectra of dibenzoborole containing pi-electron systems: controlling the electronic spectra by changing the p(pi)-pi* conjugation. , 2006, The journal of physical chemistry. A.

[43]  Sándor Suhai,et al.  Towards understanding the tandem mass spectra of protonated oligopeptides. 1: Mechanism of amide bond cleavage , 2004, Journal of the American Society for Mass Spectrometry.

[44]  K. Biemann Appendix 5. Nomenclature for peptide fragment ions (positive ions). , 1990, Methods in enzymology.