All Faculty and Research Staff Publications

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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.
Yang C, Park AC, Davis NA, Russell JD, Kim B, Brand DD, Lawrence MJ, Ge Y, Westphall MS, Coon JJ, et al. Comprehensive Mass Spectrometric Mapping of the Hydroxylated Amino Acid residues of the α1(V) Collagen Chain. Journal of Biological Chemistry. 2012 ;287:40598-40610.
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.
Ledvina AR, Lee MV, McAlister GC, Westphall MS, Coon JJ. Infrared Multiphoton Dissociation for Quantitative Shotgun Proteomics. Analytical Chemistry. 2012 ;84:4513-4519.
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.
Peterson AC, Russell JD, Bailey DJ, Westphall MS, Coon JJ. Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics. Molecular & Cellular Proteomics. 2012 ;11:1475-1488.
Brumbaugh J, Hou ZG, Russell JD, Howden SE, Yu PZ, Ledvina AR, Coon JJ, Thomson JA. Phosphorylation regulates human OCT4. Proceedings of the National Academy of Sciences of the United States of America. 2012 ;109:7162-7168.
Volkening JD, Bailey DJ, Rose CM, Grimsrud PA, Howes-Podoll M, Venkateshwaran M, Westphall MS, Ane JM, Coon JJ, Sussman MR. A Proteogenomic Survey of the Medicago truncatula Genome. Molecular & Cellular Proteomics. 2012 ;11:933-944.
Grimsrud PA, Carson JJ, Hebert AS, Hubler SL, Niemi NM, Bailey DJ, Jochem A, Stapleton DS, Keller MP, Westphall MS, et al. A Quantitative Map of the Liver Mitochondrial Phosphoproteome Reveals Posttranslational Control of Ketogenesis. Cell Metabolism. 2012 ;16:672-683.
Rose CM, Venkateshwaran M, Volkening JD, Grimsrud PA, Maeda J, Bailey DJ, Park K, Howes-Podoll M, D. Os den, Yeun LH, et al. Rapid Phosphoproteomic and Transcriptomic Changes in the Rhizobia-legume Symbiosis. Molecular & Cellular Proteomics. 2012 ;11:724-744.
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.
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.
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.
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.
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.
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.
Russell JD, Hilger RT, Ladror DT, Tervo MA, Scalf M, Shortreed MR, Coon JJ, Smith LM. Parallel Detection of Intrinsic Fluorescence from Peptides and Proteins for Quantification during Mass Spectrometric Analysis. Analytical Chemistry. 2011 ;83:2187-2193.
Phanstiel DH, Brumbaugh J, Wenger CD, Tian S, Probasco MD, Bailey DJ, Swaney DL, Tervo MA, Bolin JM, Ruotti V, et al. Proteomic and phosphoproteomic comparison of human ES and iPS cells. Nature Methods. 2011 ;8:821-U84.
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.
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.
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.
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.
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.
Good DM, Zuerbig P, Argiles A, Bauer HW, Behrens G, Coon JJ, Dakna M, Decramer S, Delles C, Dominiczak AF, et al. Naturally Occurring Human Urinary Peptides for Use in Diagnosis of Chronic Kidney Disease. Molecular & Cellular Proteomics. 2010 ;9:2424-2437.
Grimsrud PA, Swaney DL, Wenger CD, Beauchene NA, Coon JJ. Phosphoproteomics for the Masses. ACS Chemical Biology. 2010 ;5:105-119.
Wenger CD, McAlister GC, Xia Q, Coon JJ. Sub-part-per-million Precursor and Product Mass Accuracy for High-throughput Proteomics on an Electron Transfer Dissociation-enabled Orbitrap Mass Spectrometer. Molecular & Cellular Proteomics. 2010 ;9:754-763.
Swaney DL, Wenger CD, Coon JJ. Value of Using Multiple Proteases for Large-Scale Mass Spectrometry-Based Proteomics. Journal of Proteome Research. 2010 ;9:1323-1329.
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.
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.