All Faculty and Research Staff Publications

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2017
Riley NM, Westphall MS, Coon JJ. Activated Ion-Electron Transfer Dissociation Enables Comprehensive Top-Down Protein Fragmentation. Journal of Proteome Research. 2017 ;16:2653-2659.
Jayaraman D, Richards AL, Westphall MS, Coon JJ, Ane JM. Identification of the phosphorylation targets of symbiotic receptor-like kinases using a high-throughput multiplexed assay for kinase specificity. Plant Journal. 2017 ;90:1196-1207.
Riley NM, Westphall MS, Hebert AS, Coon JJ. Implementation of Activated Ion Electron Transfer Dissociation on a Quadrupole-Orbitrap-Linear Ion Trap Hybrid Mass Spectrometer. Analytical Chemistry. 2017 ;89:6358-6366.
Potts GK, McNally RM, Blanco R, You JS, Hebert AS, Westphall MS, Coon JJ, Hornberger TA. A map of the phosphoproteomic alterations that occur after a bout of maximal-intensity contractions. Journal of Physiology-London. 2017 ;595:5209-5226.
Leach FE, Riley NM, Westphall MS, Coon JJ, Amster IJ. Negative Electron Transfer Dissociation Sequencing of Increasingly Sulfated Glycosaminoglycan Oligosaccharides on an Orbitrap Mass Spectrometer. Journal of the American Society for Mass Spectrometry. 2017 ;28:1844-1854.
Riley NM, Hebert AS, Durnberger G, Stanek F, Mechtler K, Westphall MS, Coon JJ. Phosphoproteomics with Activated Ion Electron Transfer Dissociation. Analytical Chemistry. 2017 ;89:6367-6376.
Rush MJP, Riley NM, Westphall MS, Syka JEP, Coon JJ. Sulfur Pentafluoride is a Preferred Reagent Cation for Negative Electron Transfer Dissociation. Journal of the American Society for Mass Spectrometry. 2017 ;28:1324-1332.
2016
Stefely JA, Licitra F, Laredj L, Reidenbach AG, Kemmerer ZA, Grangeray A, Jaeg-Ehret T, Minogue CE, Ulbrich A, Hutchins PD, et al. Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity. Molecular Cell. 2016 ;63:608-620.
Riley NM, Mullen C, Weisbrod CR, Sharma S, Senko MW, Zabrouskov V, Westphall MS, Syka JEP, Coon JJ. Enhanced Dissociation of Intact Proteins with High Capacity Electron Transfer Dissociation. Journal of the American Society for Mass Spectrometry. 2016 ;27:520-531.
Riley NM, Bern M, Westphall MS, Coon JJ. Full-Featured Search Algorithm for Negative Electron-Transfer Dissociation. Journal of Proteome Research. 2016 ;15:2768-2776.
Stefely JA, Kwiecien NW, Freiberger EC, Richards AL, Jochem A, Rush MJP, Ulbrich A, Robinson KP, Hutchins PD, Veling MT, et al. Mitochondrial protein functions elucidated by multi-omic mass spectrometry profiling. Nature Biotechnology. 2016 ;34:1191-+.
Floyd BJ, Wilkerson EM, Veling MT, Minogue CE, Xia CW, Beebe ET, Wrobel RL, Cho H, Kremer LS, Alston CL, et al. Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function. Molecular Cell. 2016 ;63:621-632.
Potts GK, Voigt EA, Bailey DJ, Rose CM, Westphall MS, Hebert AS, Yin J, Coon JJ. Neucode Labels for Multiplexed, Absolute Protein Quantification. Analytical Chemistry. 2016 ;88:3295-3303.
Baughman JM, Rose CM, Kolumam G, Webster JD, Wilkerson EM, Merrill AE, Rhoads TW, Noubade R, Katavolos P, Lesch J, et al. NeuCode Proteomics Reveals Bap1 Regulation of Metabolism. Cell Reports. 2016 ;16:583-595.
Wilkerson EM, Johansson MW, Hebert AS, Westphall MS, Mathur SK, Jarjour NN, Schwantes EA, Mosher DF, Coon JJ. The Peripheral Blood Eosinophil Proteome. Journal of Proteome Research. 2016 ;15:1524-1533.
Marx H, Minogue CE, Jayaraman D, Richards AL, Kwiecien NW, Siahpirani AF, Rajasekar S, Maeda J, Garcia K, Del Valle-Echevarria AR, et al. A proteomic atlas of the legume Medicago truncatula and its nitrogen-fixing endosymbiont Sinorhizobium meliloti. Nature Biotechnology. 2016 ;34:1198-+.
2015
Riley NM, Westphall MS, Coon JJ. Activated Ion Electron Transfer Dissociation for Improved Fragmentation of Intact Proteins. Analytical Chemistry. 2015 ;87:7109-7116.
Rose CM, Rush MJP, Riley NM, Merrill AE, Kwiecien NW, Holden DD, Mullen C, Westphall MS, Coon JJ. A Calibration Routine for Efficient ETD in Large-Scale Proteomics. Journal of the American Society for Mass Spectrometry. 2015 ;26:1848-1857.
Zhao YM, Riley NM, Sun LL, Hebert AS, Yan XJ, Westphall MS, Rush MJP, Zhu GJ, Champion MM, Medie FM, et al. Coupling Capillary Zone Electrophoresis with Electron Transfer Dissociation and Activated Ion Electron Transfer Dissociation for Top-Down Proteomics. Analytical Chemistry. 2015 ;87:5422-5429.
Kwiecien NW, Bailey DJ, Rushp MJP, Cole JS, Ulbrich A, Hebert AS, Westphall MS, Coon JJ. High-Resolution Filtering for Improved Small Molecule Identification via GC/MS. Analytical Chemistry. 2015 ;87:8328-8335.
Minogue CE, Hebert AS, Rensvold JW, Westphall MS, Pagliarini DJ, Coon JJ. Multiplexed Quantification for Data-Independent Acquisition. Analytical Chemistry. 2015 ;87:2570-2575.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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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