All Faculty and Research Staff Publications

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2010
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.
2011
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.
2012
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.
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.
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.
2013
Ledvina AR, Rose CM, McAlister GC, Syka JEP, Westphall MS, Griep-Raming J, Schwartz JC, Coon JJ. Activated Ion ETD Performed in a Modified Collision Cell on a Hybrid QLT-Oribtrap Mass Spectrometer. Journal of the American Society for Mass Spectrometry. 2013 ;24:1623-1633.
Hebert AS, Merrill AE, Stefely JA, Bailey DJ, Wenger CD, Westphall MS, Pagliarini DJ, Coon JJ. Amine-reactive Neutron-encoded Labels for Highly Plexed Proteomic Quantitation. Molecular & Cellular Proteomics. 2013 ;12:3360-3369.
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.
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.
Russell JD, Scalf M, Book AJ, Ladror DT, Vierstra RD, Smith LM, Coon JJ. Characterization and Quantification of Intact 26S Proteasome Proteins by Real-Time Measurement of Intrinsic Fluorescence Prior to Top-down Mass Spectrometry. Plos One. 2013 ;8.
Moussavi-Harami SF, Annis DS, Ma WJ, Berry SM, Coughlin EE, Strotman LN, Maurer LM, Westphall MS, Coon JJ, Mosher DF, et al. Characterization of Molecules Binding to the 70K N-Terminal Region of Fibronectin by IFAST Purification Coupled with Mass Spectrometry. Journal of Proteome Research. 2013 ;12:3393-3404.
Frey BL, Ladror DT, Sondalle SB, Krusemark CJ, Jue AL, Coon JJ, Smith LM. Chemical Derivatization of Peptide Carboxyl Groups for Highly Efficient Electron Transfer Dissociation. Journal of the American Society for Mass Spectrometry. 2013 ;24:1710-1721.
Jackson SS, Coughlin EE, Coon JJ, Miyamoto S. Identifying post-translational modifications of NEMO by tandem mass spectrometry after high affinity purification. Protein Expression & Purification. 2013 ;92:48-53.
Rose CM, Russell JD, Ledvina AR, McAlister GC, Westphall MS, Griep-Raming J, Schwartz JC, Coon JJ, Syka JEP. Multipurpose Dissociation Cell for Enhanced ETD of Intact Protein Species. Journal of the American Society for Mass Spectrometry. 2013 ;24:816-827.
Rose CM, Merrill AE, Bailey DJ, Hebert AS, Westphall MS, Coon JJ. Neutron Encoded Labeling for Peptide Identification. Analytical Chemistry. 2013 ;85:5129-5137.
Hebert AS, Merrill AE, Bailey DJ, Still AJ, Westphall MS, Strieter ER, Pagliarini DJ, Coon JJ. Neutron-encoded mass signatures for multiplexed proteome quantification. Nature Methods. 2013 ;10:332-+.
Richards AL, Vincent CE, Guthals A, Rose CM, Westphall MS, Bandeira N, Coon JJ. Neutron-encoded Signatures Enable Product Ion Annotation From Tandem Mass Spectra. Molecular & Cellular Proteomics. 2013 ;12:3812-3823.
Wenger CD, Coon JJ. A Proteomics Search Algorithm Specifically Designed for High-Resolution Tandem Mass Spectra. Journal of Proteome Research. 2013 ;12:1377-1386.
Still AJ, Floyd BJ, Hebert AS, Bingman CA, Carson JJ, Gunderson DR, Dolan BK, Grimsrud PA, Dittenhafer-Reed KE, Stapleton DS, et al. Quantification of Mitochondrial Acetylation Dynamics Highlights Prominent Sites of Metabolic Regulation. Journal of Biological Chemistry. 2013 ;288:26209-26219.
Merrill AE, Coon JJ. Quantifying proteomes and their post-translational modifications by stable isotope label-based mass spectrometry. Current Opinion in Chemical Biology. 2013 ;17:779-786.
Vincent CE, Potts GK, Ulbrich A, Westphall MS, Atwood JA, Coon JJ, Weatherly DB. Segmentation of Precursor Mass Range Using "Tiling" Approach Increases Peptide Identifications for MS1-Based Label-Free Quantification. Analytical Chemistry. 2013 ;85:2825-2832.

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