All Faculty and Research Staff Publications

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2014
Keating DH, Zhang YP, Ong IM, McIlwain S, Morales EH, Grass JA, Tremaine M, Bothfeld W, Higbee A, Ulbrich A, et al. Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification. Frontiers in Microbiology. 2014 ;5.
Hooper C, Jackson SS, Coughlin EE, Coon JJ, Miyamoto S. Covalent Modification of the NF-kappa B Essential Modulator (NEMO) by a Chemical Compound Can Regulate Its Ubiquitin Binding Properties in Vitro. Journal of Biological Chemistry. 2014 ;289:33161-33174.
Peterson AC, Hauschild JP, Quarmby ST, Krumwiede D, Lange O, Lemke RAS, Grosse-Coosmann F, Horning S, Donohue TJ, Westphall MS, et al. Development of a GC/Quadrupole-Orbitrap Mass Spectrometer, Part I: Design and Characterization. Analytical Chemistry. 2014 ;86:10036-10043.
Peterson AC, Balloon AJ, Westphall MS, Coon JJ. Development of a GC/Quadrupole-Orbitrap Mass Spectrometer, Part II: New Approaches for Discovery Metabolomics. Analytical Chemistry. 2014 ;86:10044-10051.
Parreiras LS, Breuer RJ, Narasimhan RA, Higbee AJ, La Reau A, Tremaine M, Qin L, Willis LB, Bice BD, Bonfert BL, et al. Engineering and Two-Stage Evolution of a Lignocellulosic Hydrolysate-Tolerant Saccharomyces cerevisiae Strain for Anaerobic Fermentation of Xylose from AFEX Pretreated Corn Stover. Plos One. 2014 ;9.
Honarpour N, Rose CM, Brumbaugh J, Anderson J, Graham RLJ, Sweredoski MJ, Hess S, Coon JJ, Deshaies RJ. F-box Protein FBXL16 Binds PP2A-B55 and Regulates Differentiation of Embryonic Stem Cells along the FLK1 Lineage. Molecular & Cellular Proteomics. 2014 ;13:780-791.
Rahimi A, Ulbrich A, Coon JJ, Stahl SS. Formic-acid-induced depolymerization of oxidized lignin to aromatics. Nature. 2014 ;515:249-52.
Bailey DJ, McDevitt MT, Westphall MS, Pagliarini DJ, Coon JJ. Intelligent Data Acquisition Blends Targeted and Discovery Methods. Journal of Proteome Research. 2014 ;13:2152-2161.
Lohman DC, Forouhar F, Beebe ET, Stefely MS, Minogue CE, Ulbrich A, Stefely JA, Sukumar S, Luna-Sanchez M, Jochem A, et al. Mitochondrial COQ9 is a lipid-binding protein that associates with COQ7 to enable coenzyme Q biosynthesis. Proceedings of the National Academy of Sciences of the United States of America. 2014 ;111:E4697-E4705.
Dingley SD, Polyak E, Ostrovsky J, Srinivasan S, Lee I, Rosenfeld AB, Tsukikawa M, Xiao R, Selak MA, Coon JJ, et al. Mitochondrial DNA Variant in COX1 Subunit Significantly Alters Energy Metabolism of Geographically Divergent Wild Isolates in Caenorhabditis elegans. Journal of Molecular Biology. 2014 ;426:2199-2216.
Brumbaugh J, Russell JD, Yu PZ, Westphall MS, Coon JJ, Thomson JA. NANOG Is Multiply Phosphorylated and Directly Modified by ERK2 and CDK1 In Vitro. Stem Cell Reports. 2014 ;2:18-25.
Merrill AE, Hebert AS, MacGilvray ME, Rose CM, Bailey DJ, Bradley JC, Wood WW, M. Masri E, Westphall MS, Gasch AP, et al. NeuCode Labels for Relative Protein Quantification. Molecular & Cellular Proteomics. 2014 ;13:2503-2512.
Rhoads TW, Rose CM, Bailey DJ, Riley NM, Molden RC, Nestler AJ, Merrill AE, Smith LM, Hebert AS, Westphall MS, et al. Neutron-Encoded Mass Signatures for Quantitative Top-Down Proteomics. Analytical Chemistry. 2014 ;86:2314-2319.
Ulbrich A, Merrill AE, Hebert AS, Westphall MS, Keller MP, Attie AD, Coon JJ. Neutron-Encoded Protein Quantification by Peptide Carbamylation. Journal of the American Society for Mass Spectrometry. 2014 ;25:6-9.
Hebert AS, Richards AL, Bailey DJ, Ulbrich A, Coughlin EE, Westphall MS, Coon JJ. The One Hour Yeast Proteome. Molecular & Cellular Proteomics. 2014 ;13:339-347.
Ulbrich A, Bailey DJ, Westphall MS, Coon JJ. Organic Acid Quantitation by NeuCode Methylamidation. Analytical Chemistry. 2014 ;86:4402-4408.
Sun LL, Hebert AS, Yan XJ, Zhao YM, Westphall MS, Rush MJP, Zhu GJ, Champion MM, Coon JJ, Dovichi NJ. Over 10000 Peptide Identifications from the HeLa Proteome by Using Single-Shot Capillary Zone Electrophoresis Combined with Tandem Mass Spectrometry. Angewandte Chemie-International Edition. 2014 ;53:13931-13933.
Chasman D, Ho YH, Berry DB, Nemec CM, MacGilvray ME, Hose J, Merrill AE, Lee MV, Will JL, Coon JJ, et al. Pathway connectivity and signaling coordination in the yeast stress-activated signaling network. Molecular Systems Biology. 2014 ;10.
Bhatnagar S, Soni MS, Wrighton LS, Hebert AS, Zhou AS, Paul PK, Gregg T, Rabaglia ME, Keller MP, Coon JJ, et al. Phosphorylation and Degradation of Tomosyn-2 De-represses Insulin Secretion. Journal of Biological Chemistry. 2014 ;289:25276-25286.
Lemke RAS, Peterson AC, Ziegelhoffer EC, Westphall MS, Tjellstrom H, Coon JJ, Donohue TJ. Synthesis and scavenging role of furan fatty acids. Proceedings of the National Academy of Sciences of the United States of America. 2014 ;111:E3450-E3457.
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.
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.

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