All Department Publications

Found 88 results
Author Title [ Type(Desc)] Year
Filters: Author is Coon, J. J.  [Clear All Filters]
Journal Article
Ledvina AR, Beauchene NA, McAlister GC, Syka JEP, Schwartz JC, Griep-Raming J, Westphall MS, Coon JJ. Activated-Ion Electron Transfer Dissociation Improves the Ability of Electron Transfer Dissociation to Identify Peptides in a Complex Mixture. Analytical Chemistry. 2010;82:10068-10074.
Good DM, Coon JJ. Advancing proteomics with ion/ion chemistry. BioTechniques. 2006;40:783.
Chi A, Huttenhower C, Geer LY, Coon JJ, Syka JEP, Bai DL, Shabanowitz J, Burke DJ, Troyanskaya OG, Hunt DF. Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc Natl Acad Sci U S A. 2007;104(7):2193-8.
McAlister GC, Phanstiel D, Wenger CD, Lee VM, Coon JJ. Analysis of Tandem Mass Spectra by FTMS for Improved Large-Scale Proteomics with Superior Protein Quantification. Analytical Chemistry. 2010;82:316-322.
McAlister GC, Russell JD, Rumachik NG, Hebert AS, Syka JEP, Geer LY, Westphall MS, Pagliarini DJ, Coon JJ. Analysis of the Acidic Proteome with Negative Electron-Transfer Dissociation Mass Spectrometry. Analytical Chemistry. 2012;84:2875-2882.
Coon JJ, Syka JEP, Schwartz JC, Shabanowitz J, Hunt DF. Anion dependence in the partitioning between proton and electron transfer in ion/ion reactions. International Journal of Mass Spectrometry. 2004;236:33-42.
Coon JJ, McHale KJ, Harrison WW. Atmospheric pressure laser desorption/chemical ionization mass spectrometry: a new ionization method based on existing themes. Rapid Communications in Mass Spectrometry. 2002;16:681-685.
Vincent CE, Rensvold JW, Westphall MS, Pagliarini DJ, Coon JJ. Automated Gas-Phase Purification for Accurate, Multiplexed Quantification on a Stand-Alone Ion-Trap Mass Spectrometer. Analytical Chemistry. 2013;85:2079-2086.
Good DM, Thongboonkerd V, Novak J, Bascands J-L, Schanstra JP, Coon JJ, Dominiczak A, Mischak H. Body fluid proteomics for biomarker discovery: Lessons from the past hold the key to success in the future. Journal of Proteome Research. 2007;6:4549-4555.
Hebert AS, Dittenhafer-Reed KE, Yu W, Bailey DJ, Selen ES, Boersma MD, Carson JJ, Tonelli M, Balloon AJ, Higbee AJ, et al. Calorie Restriction and SIRT3 Trigger Global Reprogramming of the Mitochondrial Protein Acetylome. Molecular Cell. 2013;49:186-199.
Mischak H, Coon JJ, Novak J, Weissinger EM, Schanstra JP, Dominiczak AF. Capillary Electrophoresis-Mass Spectrometry as a Powerful Tool in Biomarker Discovery and Clinical Diagnosis: An Update of Recent Developments. Mass Spectrometry Reviews. 2009;28:703-724.
Chung TW, Hui RJ, Ledvina A, Coon JJ, Turecek F. Cascade Dissociations of Peptide Cation-Radicals. Part 1. Scope and Effects of Amino Acid Residues in Penta-, Nona-, and Decapeptides. Journal of the American Society for Mass Spectrometry. 2012;23:1336-1350.
Ledvina AR, Chung TW, Hui RJ, Coon JJ, Turecek F. Cascade Dissociations of Peptide Cation-Radicals. Part 2. Infrared Multiphoton Dissociation and Mechanistic Studies of z-Ions from Pentapeptides. Journal of the American Society for Mass Spectrometry. 2012;23:1351-1363.
Coon JJ, Zuerbig P, Dakna M, Dominicza AF, Decramer S, Fliser D, Frommberger M, Golovko I, Good DM, Herget-Rosenthal S, et al. CE-MS analysis of the human urinary proteome for biomarker discovery and disease diagnostics. Proteomics Clinical Applications. 2008;2:964-973.
Xia Q, Lee VM, Rose CM, Marsh AJ, Hubler SL, Wenger CD, Coon JJ. Characterization and Diagnostic Value of Amino Acid Side Chain Neutral Losses Following Electron-Transfer Dissociation. Journal of the American Society for Mass Spectrometry. 2011;22:255-264.
Rumachik NG, McAlister GC, Russell JD, Bailey DJ, Wenger CD, Coon JJ. Characterizing Peptide Neutral Losses Induced by Negative Electron-Transfer Dissociation (NETD). Journal of the American Society for Mass Spectrometry. 2012;23:718-727.
Coon JJ. Collisions or electrons? Protein sequence analysis in the 21st century. Anal Chem. 2009;81(9):3208-15.
Wenger CD, Phanstiel DH, Lee VM, Bailey DJ, Coon JJ. COMPASS: A suite of pre- and post-search proteomics software tools for OMSSA. Proteomics. 2011;11:1064-1074.
Swaney DL, McAlister GC, Coon JJ. Decision tree-driven tandem mass spectrometry for shotgun proteomics. Nature Methods. 2008;5:959-964.
Peterson AC, McAlister GC, Quarmby ST, Griep-Raming J, Coon JJ. Development and Characterization of a GC-Enabled QLT-Orbitrap for High-Resolution and High-Mass Accuracy GC/MS. Analytical Chemistry. 2010;82:8618-8628.
Coon JJ, Steele HA, Laipis PJ, Harrison WW. Direct atmospheric pressure coupling of polyacrylamide gel electrophoresis to mass spectrometry for rapid protein sequence analysis. Journal of Proteome Research. 2003;2:610-617.
Theodorescu D, Schiffer E, Bauer HW, Douwes F, Eichhorn F, Polley R, Schmidt T, Schoefer W, Zuerbig P, Good DM, et al. Discovery and validation of urinary biomarkers for propstate cancer. Proteomics Clinical Applications. 2008;2:556-570.
Williams KD, McAlister GC, Good DM, Coon JJ, Muddiman DC. Dual electrospray ion source for electron-transfer dissociation on a hybrid linear ion trap-orbitrap mass spectrometer. Anal Chem. 2007;79(20):7916-9.
Second TP, Blethrow JD, Schwartz JC, Merrihew GE, MacCoss MJ, Swaney DL, Russell JD, Coon JJ, Zabrouskov V. Dual-Pressure Linear Ion Trap Mass Spectrometer Improving the Analysis of Complex Protein Mixtures. Analytical Chemistry. 2009;81:7757-7765.
Lee VM, Topper SE, Hubler SL, Hose J, Wenger CD, Coon JJ, Gasch AP. A dynamic model of proteome changes reveals new roles for transcript alteration in yeast. Molecular Systems Biology. 2011;7 514 514.
Good DM, Wenger CD, Coon JJ. The effect of interfering ions on search algorithm performance for electron-transfer dissociation data. Proteomics. 2010;10:164-167.
Coon JJ, Shabanowitz J, Hunt DF, Syka JEP. Electron transfer dissociation of peptide anions. Journal of the American Society for Mass Spectrometry. 2005;16:880-882.
Julian BA, Wittke S, Novak J, Good DM, Coon JJ, Kellmann M, Zuerbig P, Schiffer E, Haubitz M, Moldoveanu Z, et al. Electrophoretic methods for analysis of urinary polypeptides in IgA-associated renal diseases. Electrophoresis. 2007;28:4469-4483.
Julian BA, Wittke S, Novak J, Good DM, Coon JJ, Kellmann M, Zürbig P, Schiffer E, Haubitz M, Moldoveanu Z, et al. Electrophoretic methods for analysis of urinary polypeptides in IgA-associated renal diseases. Electrophoresis. 2007;28(23):4469-83.
Wenger CD, Lee VM, Hebert AS, McAlister GC, Phanstiel DH, Westphall MS, Coon JJ. Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging. Nature Methods. 2011;8:933-935.
McAlister GC, Phanstiel DH, Brumbaugh J, Westphall MS, Coon JJ. Higher-energy Collision-activated Dissociation Without a Dedicated Collision Cell. Molecular & Cellular Proteomics. 2011;10.
Mednikov EG, Dahl LF, Peterson AC, Russell JD, Bailey DJ, Westphall MS, Coon JJ. How innocent is thallium(I)? Corrected formulations of Tl2Pd14(CO)(9)(PMe3)(11) PF6 (2) and TlPd9(CO)(9)(PPh3)(6) PF6 clusters previously reported as corresponding Au2Pd14 and AuPd9 clustersParallel Reaction Monitoring for High Resolution and High Mass Ac. Chemical Communications. 2013;49:1085-1087.
Swaney DL, Wenger CD, Thomson JA, Coon JJ. Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America. 2009;106:995-1000.
Van Etten J, Schagat TL, Hrit J, Weidmann CA, Brumbaugh J, Coon JJ, Goldstrohm AC. Human Pumilio Proteins Recruit Multiple Deadenylases to Efficiently Repress Messenger RNAs. Journal of Biological Chemistry. 2012;287:36370-36383.
Zürbig P, Decramer S, Dakna M, Jantos J, Good DM, Coon JJ, Bandin F, Mischak H, Bascands J-L, Schanstra JP. The human urinary proteome reveals high similarity between kidney aging and chronic kidney disease. Proteomics. 2009;9(8):2108-17.
Tainter CJ, Ni Y, Shi L, Skinner JL, Mednikov EG, Dahl LF, Peterson AC, Russell JD, Bailey DJ, Westphall MS, et al. Hydrogen Bonding and OH-Stretch Spectroscopy in Water: Hexamer (Cage), Liquid Surface, Liquid, and IceHow innocent is thallium(I)? Corrected formulations of Tl2Pd14(CO)(9)(PMe3)(11) PF6 (2) and TlPd9(CO)(9)(PPh3)(6) PF6 clusters previously reported as cor. Journal of Physical Chemistry Letters. 2013;4:12-17.
Haubitz M, Good DM, Woywodt A, Haller H, Rupprecht H, Theodorescu D, Dakna M, Coon JJ, Mischak H. Identification and Validation of Urinary Biomarkers for Differential Diagnosis and Evaluation of Therapeutic Intervention in Anti-neutrophil Cytoplasmic Antibody-associated Vasculitis. Molecular & Cellular Proteomics. 2009;8:2296-2307.
McAlister GC, Phanstiel D, Good DM, Berggren TW, Coon JJ. Implementation of electron-transfer dissociation on a hybrid linear ion trap-orbitrap mass spectrometer. Analytical Chemistry. 2007;79:3525-3534.
Vasicek LA, Ledvina AR, Shaw J, Griep-Raming J, Westphall MS, Coon JJ, Brodbelt JS. Implementing Photodissociation in an Orbitrap Mass Spectrometer. Journal of the American Society for Mass Spectrometry. 2011;22:1105-1108.
McAlister GC, Kiessel SEB, Coon JJ. In vacuo formation of peptide-metal coordination complexes. International Journal of Mass Spectrometry. 2008;276:149-152.
Ledvina AR, Savitski MM, Zubarev AR, Good DM, Coon JJ, Zubarev RA. Increased Throughput of Proteomics Analysis by Multiplexing High-Resolution Tandem Mass Spectra. Analytical Chemistry. 2011;83:7651-7656.
Tan YZ, Jin S, Hamers RJ, Tainter CJ, Ni Y, Shi L, Skinner JL, Mednikov EG, Dahl LF, Peterson AC, et al. Influence of Hole-Sequestering Ligands on the Photostability of CdSe Quantum DotsHydrogen Bonding and OH-Stretch Spectroscopy in Water: Hexamer (Cage), Liquid Surface, Liquid, and IceHow innocent is thallium(I)? Corrected formulations of Tl2Pd14(CO)(9)(PM. Journal of Physical Chemistry C. 2013;117:313-320.
Ledvina AR, Lee MV, McAlister GC, Westphall MS, Coon JJ. Infrared Multiphoton Dissociation for Quantitative Shotgun Proteomics. Analytical Chemistry. 2012;84:4513-4519.
Gardner MW, Smith SI, Ledvina AR, Madsen JA, Coon JJ, Schwartz JC, Stafford GC, Brodbelt JS. Infrared Multiphoton Dissociation of Peptide Cations in a Dual Pressure Linear Ion Trap Mass Spectrometer. Analytical Chemistry. 2009;81:8109-8118.
Ledvina AR, McAlister GC, Gardner MW, Smith SI, Madsen JA, Schwartz JC, Stafford, George C. J, Syka JEP, Brodbelt JS, Coon JJ. Infrared Photoactivation Reduces Peptide Folding and Hydrogen-Atom Migration following ETD Tandem Mass Spectrometry. Angewandte Chemie-International Edition. 2009;48:8526-8528.
Bailey DJ, Rose CM, McAlister GC, Brumbaugh J, Yu PZ, Wenger CD, Westphall MS, Thomson JA, Coon JJ. Instant spectral assignment for advanced decision tree-driven mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America. 2012;109:8411-8416.
Bailey DJ, Rose CM, McAlister GC, Brumbaugh J, Yu PZ, Wenger CD, Westphall MS, Thomson JA, Coon JJ. Instant spectral assignment for advanced decision tree-driven mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America. 2012;109:8411-8416.
Xia Q, Good DM, Wenger CD, Coon JJ. Intellinsity: a tool for visualization and analysis of liquid chromatography/tandem mass spectrometry sampling events. Rapid Communications in Mass Spectrometry. 2010;24:3217-3218.
Frey BL, Krusemark CJ, Ledvina AR, Coon JJ, Belshaw PJ, Smith LM. Ion-ion reactions with fixed-charge modified proteins to produce ions in a single, very high charge state. International Journal of Mass Spectrometry. 2008;276:136-143.
Grimsrud PA, den Os D, Wenger CD, Swaney DL, Schwartz D, Sussman MR, Ané J-M, Coon JJ. Large-scale phosphoprotein analysis in Medicago truncatula roots provides insight into in vivo kinase activity in legumes. Plant Physiol. 2010;152(1):19-28.

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