All Faculty and Research Staff Publications

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2015
Minogue CE, Hebert AS, Rensvold JW, Westphall MS, Pagliarini DJ, Coon JJ. Multiplexed Quantification for Data-Independent Acquisition. Analytical Chemistry. 2015 ;87:2570-2575.
Riley NM, Rush MJP, Rose CM, Richards AL, Kwiecien NW, Bailey DJ, Hebert AS, Westphall MS, Coon JJ. The Negative Mode Proteome with Activated Ion Negative Electron Transfer Dissociation (AI-NETD). Molecular & Cellular Proteomics. 2015 ;14:2644-2660.
Rhoads TW, Prasad A, Kwiecien NW, Merrill AE, Zawack K, Westphall MS, Schroeder FC, Kimble J, Coon JJ. NeuCode Labeling in Nematodes: Proteomic and Phosphoproteomic Impact of Ascaroside Treatment in Caenorhabditis elegans. Molecular & Cellular Proteomics. 2015 ;14:2922-2935.
Richards AL, Hebert AS, Ulbrich A, Bailey DJ, Coughlin EE, Westphall MS, Coon JJ. One-hour proteome analysis in yeast. Nature Protocols. 2015 ;10:701-714.
Mondal A, Potts GK, Dawson AR, Coon JJ, Mehle A. Phosphorylation at the Homotypic Interface Regulates Nucleoprotein Oligomerization and Assembly of the Influenza Virus Replication Machinery. Plos Pathogens. 2015 ;11.
Nguyen TT, Volkening JD, Rose CM, Venkateshwaran M, Westphall MS, Coon JJ, Ane JM, Sussman MR. Potential regulatory phosphorylation sites in a Medicago truncatula plasma membrane proton pump implicated during early symbiotic signaling in roots. FEBS Letters. 2015 ;589:2186-2193.
Huang MW, Hebert AS, Coon JJ, Hull CM. Protein Composition of Infectious Spores Reveals Novel Sexual Development and Germination Factors in Cryptococcus. Plos Genetics. 2015 ;11.
Richards AL, Merrill AE, Coon JJ. Proteome sequencing goes deep. Current Opinion in Chemical Biology. 2015 ;24:11-17.
Venkateshwaran M, Jayaraman D, Chabaud M, Genre A, Balloon AJ, Maeda J, Forshey K, D. Os den, Kwiecien NW, Coon JJ, et al. A role for the mevalonate pathway in early plant symbiotic signaling. Proceedings of the National Academy of Sciences of the United States of America. 2015 ;112:9781-9786.
Nguyen HTH, Shaffer CJ, Ledvina AR, Coon JJ, Turecek F. Serine effects on collision-induced dissociation and photodissociation of peptide cation radicals of the z(+O)-type. International Journal of Mass Spectrometry. 2015 ;378:20-30.
Tagliabracci VS, Wiley SE, Guo X, Kinch LN, Durrant E, Wen JZ, Xiao JY, Cui JX, Nguyen KB, Engel JL, et al. A Single Kinase Generates the Majority of the Secreted Phosphoproteome. Cell. 2015 ;161:1619-1632.
Dittenhafer-Reed KE, Richards AL, Fan J, Smallegan MJ, Siahpirani AF, Kemmerer ZA, Prolla TA, Roy S, Coon JJ, Denu JM. SIRT3 Mediates Multi-Tissue Coupling for Metabolic Fuel Switching. Cell Metabolism. 2015 ;21:637-646.
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.

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