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.
Chung J, Wittig JG, Ghamari A, Maeda M, Dailey TA, Bergonia H, Kafina MD, Coughlin EE, Minogue CE, Hebert AS, et al. Erythropoietin signaling regulates heme biosynthesis. eLife. 2017 ;6.
Hewitt KJ, Katsumura KR, Matson DR, Devadas P, Tanimura N, Hebert AS, Coon JJ, Kim JS, Dewey CN, Keles S, et al. GATA Factor-Regulated Samd14 Enhancer Confers Red Blood Cell Regeneration and Survival in Severe Anemia. Developmental Cell. 2017 ;42:213-+.
Shishkova E, Zeng H, Liu FB, Kwiecien NW, Hebert AS, Coon JJ, Xu W. Global mapping of CARM1 substrates defines enzyme specificity and substrate recognition. Nature Communications. 2017 ;8.
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.
Mondal A, Dawson AR, Potts GK, Freiberger EC, Baker SF, Moser LA, Bernard KA, Coon JJ, Mehle A. Influenza virus recruits host protein kinase C to control assembly and activity of its replication machinery. eLife. 2017 ;6.
Guo X, Niemi NM, Coon JJ, Pagliarini DJ. Integrative proteomics and biochemical analyses define Ptc6p as the Saccharomyces cerevisiae pyruvate dehydrogenase phosphatase. Journal of Biological Chemistry. 2017 ;292:11751-11759.
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.
Guo X, Niemi NM, Hutchins PD, Condon SGF, Jochem A, Ulbrich A, Higbee AJ, Russell JD, Senes A, Coon JJ, et al. Ptc7p Dephosphorylates Select Mitochondrial Proteins to Enhance Metabolic Function. Cell Reports. 2017 ;18:307-313.
Diaz JE, Morgan CW, Minogue CE, Hebert AS, Coon JJ, Wells JA. A Split-Abl Kinase for Direct Activation in Cells. 2017 ;24:1250-+.
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.
Lera RF, Potts GK, Suzuki A, Johnson JM, Salmon ED, Coon JJ, Burkard ME. Decoding Polo-like kinase 1 signaling along the kinetochore-centromere axis. Nature Chemical Biology. 2016 ;12:411-U61.
Sato TK, Tremaine M, Parreiras LS, Hebert AS, Myers KS, Higbee AJ, Sardi M, McIlwain SJ, Ong IM, Breuer RJ, et al. Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae. Plos Genetics. 2016 ;12.
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.
Ong RG, Higbee A, Bottoms S, Dickinson Q, Xie D, Smith SA, Serate J, Pohlmann E, Jones AD, Coon JJ, et al. Inhibition of microbial biofuel production in drought-stressed switchgrass hydrolysate. Biotechnology for Biofuels. 2016 ;9.
Dickinson Q, Bottoms S, Hinchman L, McIlwain S, Li S, Myers CL, Boone C, Coon JJ, Hebert A, Sato TK, et al. Mechanism of imidazolium ionic liquids toxicity in Saccharomyces cerevisiae and rational engineering of a tolerant, xylose-fermenting strain. Microbial Cell Factories. 2016 ;15.
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.
Weisenhorn EMM, Erve TJ van 't, Riley NM, Hess JR, Raife TJ, Coon JJ. Multi-omics Evidence for Inheritance of Energy Pathways in Red Blood Cells. Molecular & Cellular Proteomics. 2016 ;15:3614-3623.
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.
Shishkova E, Hebert AS, Coon JJ. Now, More Than Ever, Proteomics Needs Better Chromatography. Cell Systems. 2016 ;3:321-324.
Kuang MC, Hutchins PD, Russell JD, Coon JJ, Hittinger CT. Ongoing resolution of duplicate gene functions shapes the diversification of a metabolic network. eLife. 2016 ;5.
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.
Riley NM, Coon JJ. Phosphoproteomics in the Age of Rapid and Deep Proteome Profiling. Analytical Chemistry. 2016 ;88:74-94.
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-+.
Riley NM, Hebert AS, Coon JJ. Proteomics Moves into the Fast Lane. Cell Systems. 2016 ;2:142-143.
Sarks C, Higbee A, Piotrowski J, Xue SS, Coon JJ, Sato TK, Jin MJ, Balan V, Dale BE. Quantifying pretreatment degradation compounds in solution and accumulated by cells during solids and yeast recycling in the Rapid Bioconversion with Integrated recycling Technology process using AFEX (TM) corn stover. Bioresource Technology. 2016 ;205:24-33.
Xue L, Blythe EE, Freiberger EC, Mamrosh JL, Hebert AS, Reitsma JM, Hess S, Coon JJ, Deshaies RJ. Valosin-containing protein (VCP)-Adaptor Interactions are Exceptionally Dynamic and Subject to Differential Modulation by a VCP Inhibitor. Molecular & Cellular Proteomics. 2016 ;15:2970-2986.
2015
Annis DS, Ma HQ, Balas DM, Kumfer KT, Sandbo N, Potts GK, Coon JJ, Mosher DF. Absence of Vitamin K-Dependent gamma-Carboxylation in Human Periostin Extracted from Fibrotic Lung or Secreted from a Cell Line Engineered to Optimize gamma-Carboxylation. Plos One. 2015 ;10.
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.
Ledvinaa AR, Coon JJ, Turecek F. Competitive hydrogen atom migrations accompanying cascade dissociations of peptide cation-radicals of the z(+center dot) type. International Journal of Mass Spectrometry. 2015 ;377:44-53.
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.
Lippmann ES, Williams CE, Ruhl DA, Estevez-Silva MC, Chapman ER, Coon JJ, Ashton RS. Deterministic HOX Patterning in Human Pluripotent Stem Cell-Derived Neuroectoderm. Stem Cell Reports. 2015 ;4:632-644.
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.
Overmyer KA, Evans CR, Qi NR, Minogue CE, Carson JJ, Chermside-Scabbo CJ, Koch LG, Britton SL, Pagliarini DJ, Coon JJ, et al. Maximal Oxidative Capacity during Exercise Is Associated with Skeletal Muscle Fuel Selection and Dynamic Changes in Mitochondrial Protein Acetylation. Cell Metabolism. 2015 ;21:468-478.
Austin S, Kontur WS, Ulbrich A, Oshlag JZ, Zhang WP, Higbee A, Zhang YP, Coon JJ, Hodge DB, Donohue TJ, et al. Metabolism of Multiple Aromatic Compounds in Corn Stover Hydrolysate by Rhodopseudomonas palustris. Environmental Science & Technology. 2015 ;49:8914-8922.
Stefely JA, Reidenbach AG, Ulbrich A, Oruganty K, Floyd BJ, Jochem A, Saunders JM, Johnson IE, Minogue CE, Wrobel RL, et al. Mitochondrial ADCK3 Employs an Atypical Protein Kinase-like Fold to Enable Coenzyme Q Biosynthesis. Molecular Cell. 2015 ;57:83-94.
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.
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.

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