All Faculty and Research Staff Publications

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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. Proceedings of the National Academy of Sciences of the United States of America. 2007 ;104:2193-2198.
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.
Williams DK, 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. Analytical Chemistry. 2007 ;79:7916-7919.
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.
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.
Swaney DL, McAlister GC, Phanstiel D, Brumbaugh J, Keith J, Ficarro SB, Feng X, Ruotti V, Stewart R, Thomson JA, et al. New technology to detect and monitor the post-translational modification events that commit human embryonic stem cells to exit the pluripotent state. Molecular & Cellular Proteomics. 2007 ;6:36-36.
Good DM, Wirtala M, McAlister GC, Coon JJ. Performance characteristics of electron transfer dissociation mass spectrometry. Molecular & Cellular Proteomics. 2007 ;6:1942-1951.
Khidekel N, Ficarro SB, Clark PM, Bryan MC, Swaney DL, Rexach JE, Sun YE, Coon JJ, Peters EC, Hsieh-Wilson LC. Probing the dynamics of O-GlcNAc glycosylation in the brain using quantitative proteomics. Nature Chemical Biology. 2007 ;3:339-348.
Swaney DL, McAlister GC, Wirtala M, Schwartz JC, Syka JEP, Coon JJ. Supplemental activation method for high-efficiency electron-transfer dissociation of doubly protonated peptide precursors. Analytical Chemistry. 2007 ;79:477-485.
Lecchi S, Nelson CJ, Allen KE, Swaney DL, Thompson KL, Coon JJ, Sussman MR, Slayman CW. Tandem phosphorylation of Ser-911 and Thr-912 at the C terminus of yeast plasma membrane H+-ATPase leads to glucose-dependent activation. Journal of Biological Chemistry. 2007 ;282:35471-35481.
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.
Swaney DL, McAlister GC, Coon JJ. Decision tree-driven tandem mass spectrometry for shotgun proteomics. Nature Methods. 2008 ;5:959-964.
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.
McAlister GC, Kiessel SEB, Coon JJ. In vacuo formation of peptide-metal coordination complexes. International Journal of Mass Spectrometry. 2008 ;276:149-152.
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.
Phanstiel D, Brumbaugh J, Berggren TW, Conard K, Feng X, Levenstein ME, McAlister GC, Thomson JA, Coon JJ. Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells. Proceedings of the National Academy of Sciences of the United States of America. 2008 ;105:4093-4098.
Phanstiel D, Zhang Y, Marto JA, Coon JJ. Peptide and protein quantification using iTRAQ with electron transfer dissociation. Journal of the American Society for Mass Spectrometry. 2008 ;19:1255-1262.
McAlister GC, Berggren TW, Griep-Raming J, Horning S, Makarov A, Phanstiel D, Stafford G, Swaney DL, Syka JEP, Zabrouskov V, et al. A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer. Journal of Proteome Research. 2008 ;7:3127-3136.
Brumbaugh J, Phanstiel D, Coon JJ. Unraveling the histone's potential A proteomics perspective. Epigenetics. 2008 ;3:254-257.
Zimmerli LU, Schiffer E, Zuerbig P, Good DM, Kellmann M, Mouls L, Pitt AR, Coon JJ, Schmieder RE, Peter KH, et al. Urinary proteomic biomarkers on coronary artery disease. Molecular & Cellular Proteomics. 2008 ;7:290-298.
Rossing K, Mischak H, Dakna M, Zuerbig P, Novak J, Julian BA, Good DM, Coon JJ, Tarnow L, Rossing P. Urinary proteomics in diabetes and CKD. Journal of the American Society of Nephrology. 2008 ;19:1283-1290.
Hubler SL, Jue A, Keith J, McAlister GC, Craciun G, Coon JJ. Valence parity renders z(center dot)-type ions chemically distinct. Journal of the American Chemical Society. 2008 ;130:6388-6394.
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.
Coon JJ. Collisions or Electrons? Protein Sequence Analysis in the 21st Century. Analytical Chemistry. 2009 ;81:3208-3215.
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.
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.
Zurbig P, Decramer S, Dakna M, Jantos J, Good DM, Coon JJ, Bandin F, Mischak H, Bascands JL, Schanstra JP. The human urinary proteome reveals high similarity between kidney aging and chronic kidney disease. Proteomics. 2009 ;9:2108-2117.
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.
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.
Good DM, Coon JJ. Mass Spectrometric Analysis of Body Fluids for Biomarker Discovery. In: Ottens AK, Wang KKW Vol. 566. ; 2009. pp. 277-291.
Sadygov RG, Good DM, Swaney DL, Coon JJ. A New Probabilistic Database Search Algorithm for ETD Spectra. Journal of Proteome Research. 2009 ;8:3198-3205.
Phanstiel D, Unwin R, McAlister GC, Coon JJ. Peptide Quantification Using 8-Plex Isobaric Tags and Electron Transfer Dissociation Tandem Mass Spectrometry. Analytical Chemistry. 2009 ;81:1693-1698.
Duellman SJ, Thompson KL, Coon JJ, Burgess RR. Phosphorylation sites of Epstein-Barr virus EBNA1 regulate its function. Journal of General Virology. 2009 ;90:2251-2259.
Good DM, Wenger CD, McAlister GC, Bai DL, Hunt DF, Coon JJ. Post-Acquisition ETD Spectral Processing for Increased Peptide Identifications. Journal of the American Society for Mass Spectrometry. 2009 ;20:1435-1440.
Madsen JA, Gardner MW, Smith SI, Ledvina AR, Coon JJ, Schwartz JC, Stafford, George C. J, Brodbelt JS. Top-Down Protein Fragmentation by Infrared Multiphoton Dissociation in a Dual Pressure Linear Ion Trap. Analytical Chemistry. 2009 ;81:8677-8686.
McGivern JV, Swaney DL, Coon JJ, Sheets MD. Toward Defining the Phosphoproteome of Xenopus laevis Embryos. Developmental Dynamics. 2009 ;238:1433-1443.