Publications

Guo X, Niemi NM, Hutchins PD, Condon SGF, Jochem A, Ulbrich A, et al.. Ptc7p Dephosphorylates Select Mitochondrial Proteins to Enhance Metabolic Function. Cell Reports. 2017;18:307-313.
Shishkova E, Zeng H, Liu FB, Kwiecien NW, Hebert AS, Coon JJ, et al.. 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.
Chung J, Wittig JG, Ghamari A, Maeda M, Dailey TA, Bergonia H, et al.. Erythropoietin signaling regulates heme biosynthesis. eLife. 2017;6.
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.
Riley NM, Hebert AS, Durnberger G, Stanek F, Mechtler K, Westphall MS, et al.. 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.
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.
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.
Potts GK, McNally RM, Blanco R, You JS, Hebert AS, Westphall MS, et al.. A map of the phosphoproteomic alterations that occur after a bout of maximal-intensity contractions. Journal of Physiology-London. 2017;595:5209-5226.
Hewitt KJ, Katsumura KR, Matson DR, Devadas P, Tanimura N, Hebert AS, et al.. GATA Factor-Regulated Samd14 Enhancer Confers Red Blood Cell Regeneration and Survival in Severe Anemia. Developmental Cell. 2017;42:213-+.
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.
Mondal A, Dawson AR, Potts GK, Freiberger EC, Baker SF, Moser LA, et al.. Influenza virus recruits host protein kinase C to control assembly and activity of its replication machinery. eLife. 2017;6.
Riley NM, Coon JJ. Phosphoproteomics in the Age of Rapid and Deep Proteome Profiling. Analytical Chemistry. 2016;88:74-94.
Dickinson Q, Bottoms S, Hinchman L, McIlwain S, Li S, Myers CL, 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.
Sarks C, Higbee A, Piotrowski J, Xue SS, Coon JJ, Sato TK, et al.. 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.
Riley NM, Mullen C, Weisbrod CR, Sharma S, Senko MW, Zabrouskov V, et al.. Enhanced Dissociation of Intact Proteins with High Capacity Electron Transfer Dissociation. Journal of the American Society for Mass Spectrometry. 2016;27:520-531.
Potts GK, Voigt EA, Bailey DJ, Rose CM, Westphall MS, Hebert AS, et al.. Neucode Labels for Multiplexed, Absolute Protein Quantification. Analytical Chemistry. 2016;88:3295-3303.
Wilkerson EM, Johansson MW, Hebert AS, Westphall MS, Mathur SK, Jarjour NN, et al.. The Peripheral Blood Eosinophil Proteome. Journal of Proteome Research. 2016;15:1524-1533.
Lera RF, Potts GK, Suzuki A, Johnson JM, Salmon ED, Coon JJ, et al.. Decoding Polo-like kinase 1 signaling along the kinetochore-centromere axis. Nature Chemical Biology. 2016;12:411-U61.
Baughman JM, Rose CM, Kolumam G, Webster JD, Wilkerson EM, Merrill AE, et al.. NeuCode Proteomics Reveals Bap1 Regulation of Metabolism. Cell Reports. 2016;16:583-595.
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.
Floyd BJ, Wilkerson EM, Veling MT, Minogue CE, Xia CW, Beebe ET, et al.. Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function. Molecular Cell. 2016;63:621-632.
Stefely JA, Licitra F, Laredj L, Reidenbach AG, Kemmerer ZA, Grangeray A, et al.. Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity. Molecular Cell. 2016;63:608-620.
Xue L, Blythe EE, Freiberger EC, Mamrosh JL, Hebert AS, Reitsma JM, et al.. 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.
Sato TK, Tremaine M, Parreiras LS, Hebert AS, Myers KS, Higbee AJ, et al.. Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae. Plos Genetics. 2016;12.
Stefely JA, Kwiecien NW, Freiberger EC, Richards AL, Jochem A, Rush MJP, et al.. Mitochondrial protein functions elucidated by multi-omic mass spectrometry profiling. Nature Biotechnology. 2016;34:1191-+.
Marx H, Minogue CE, Jayaraman D, Richards AL, Kwiecien NW, Siahpirani AF, et al.. A proteomic atlas of the legume Medicago truncatula and its nitrogen-fixing endosymbiont Sinorhizobium meliloti. Nature Biotechnology. 2016;34:1198-+.
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.
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.
Riley NM, Hebert AS, Coon JJ. Proteomics Moves into the Fast Lane. Cell Systems. 2016;2:142-143.
Shishkova E, Hebert AS, Coon JJ. Now, More Than Ever, Proteomics Needs Better Chromatography. Cell Systems. 2016;3:321-324.
Ong RG, Higbee A, Bottoms S, Dickinson Q, Xie D, Smith SA, et al.. Inhibition of microbial biofuel production in drought-stressed switchgrass hydrolysate. Biotechnology for Biofuels. 2016;9.
Stefely JA, Reidenbach AG, Ulbrich A, Oruganty K, Floyd BJ, Jochem A, et al.. Mitochondrial ADCK3 Employs an Atypical Protein Kinase-like Fold to Enable Coenzyme Q Biosynthesis. Molecular Cell. 2015;57:83-94.
Richards AL, Merrill AE, Coon JJ. Proteome sequencing goes deep. Current Opinion in Chemical Biology. 2015;24:11-17.
Minogue CE, Hebert AS, Rensvold JW, Westphall MS, Pagliarini DJ, Coon JJ. Multiplexed Quantification for Data-Independent Acquisition. Analytical Chemistry. 2015;87:2570-2575.
Overmyer KA, Evans CR, Qi NR, Minogue CE, Carson JJ, Chermside-Scabbo CJ, 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.
Dittenhafer-Reed KE, Richards AL, Fan J, Smallegan MJ, Siahpirani AF, Kemmerer ZA, et al.. SIRT3 Mediates Multi-Tissue Coupling for Metabolic Fuel Switching. Cell Metabolism. 2015;21:637-646.
Lippmann ES, Williams CE, Ruhl DA, Estevez-Silva MC, Chapman ER, Coon JJ, et al.. Deterministic HOX Patterning in Human Pluripotent Stem Cell-Derived Neuroectoderm. Stem Cell Reports. 2015;4:632-644.
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.
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.
Richards AL, Hebert AS, Ulbrich A, Bailey DJ, Coughlin EE, Westphall MS, et al.. One-hour proteome analysis in yeast. Nature Protocols. 2015;10:701-714.
Zhao YM, Riley NM, Sun LL, Hebert AS, Yan XJ, Westphall MS, 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.
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.
Tagliabracci VS, Wiley SE, Guo X, Kinch LN, Durrant E, Wen JZ, et al.. A Single Kinase Generates the Majority of the Secreted Phosphoproteome. Cell. 2015;161:1619-1632.
Venkateshwaran M, Jayaraman D, Chabaud M, Genre A, Balloon AJ, Maeda J, 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 TT, Volkening JD, Rose CM, Venkateshwaran M, Westphall MS, Coon JJ, et al.. 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.
Riley NM, Westphall MS, Coon JJ. Activated Ion Electron Transfer Dissociation for Improved Fragmentation of Intact Proteins. Analytical Chemistry. 2015;87:7109-7116.
Austin S, Kontur WS, Ulbrich A, Oshlag JZ, Zhang WP, Higbee A, et al.. Metabolism of Multiple Aromatic Compounds in Corn Stover Hydrolysate by Rhodopseudomonas palustris. Environmental Science & Technology. 2015;49:8914-8922.
Kwiecien NW, Bailey DJ, Rushp MJP, Cole JS, Ulbrich A, Hebert AS, et al.. High-Resolution Filtering for Improved Small Molecule Identification via GC/MS. Analytical Chemistry. 2015;87:8328-8335.
Annis DS, Ma HQ, Balas DM, Kumfer KT, Sandbo N, Potts GK, et al.. 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.
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.
Rose CM, Rush MJP, Riley NM, Merrill AE, Kwiecien NW, Holden DD, et al.. A Calibration Routine for Efficient ETD in Large-Scale Proteomics. Journal of the American Society for Mass Spectrometry. 2015;26:1848-1857.
Rhoads TW, Prasad A, Kwiecien NW, Merrill AE, Zawack K, Westphall MS, et al.. NeuCode Labeling in Nematodes: Proteomic and Phosphoproteomic Impact of Ascaroside Treatment in Caenorhabditis elegans. Molecular & Cellular Proteomics. 2015;14:2922-2935.
Ulbrich A, Merrill AE, Hebert AS, Westphall MS, Keller MP, Attie AD, et al.. Neutron-Encoded Protein Quantification by Peptide Carbamylation. Journal of the American Society for Mass Spectrometry. 2014;25:6-9.
Ulbrich A, Bailey DJ, Westphall MS, Coon JJ. Organic Acid Quantitation by NeuCode Methylamidation. Analytical Chemistry. 2014;86:4402-4408.
Rhoads TW, Rose CM, Bailey DJ, Riley NM, Molden RC, Nestler AJ, et al.. Neutron-Encoded Mass Signatures for Quantitative Top-Down Proteomics. Analytical Chemistry. 2014;86:2314-2319.
Lemke RAS, Peterson AC, Ziegelhoffer EC, Westphall MS, Tjellstrom H, Coon JJ, et al.. 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.
Merrill AE, Hebert AS, MacGilvray ME, Rose CM, Bailey DJ, Bradley JC, et al.. NeuCode Labels for Relative Protein Quantification. Molecular & Cellular Proteomics. 2014;13:2503-2512.
Parreiras LS, Breuer RJ, Narasimhan RA, Higbee AJ, La Reau A, Tremaine M, 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.
Bhatnagar S, Soni MS, Wrighton LS, Hebert AS, Zhou AS, Paul PK, et al.. Phosphorylation and Degradation of Tomosyn-2 De-represses Insulin Secretion. Journal of Biological Chemistry. 2014;289:25276-25286.
Peterson AC, Hauschild JP, Quarmby ST, Krumwiede D, Lange O, Lemke RAS, 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.
Lohman DC, Forouhar F, Beebe ET, Stefely MS, Minogue CE, Ulbrich 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.
Sun LL, Hebert AS, Yan XJ, Zhao YM, Westphall MS, Rush MJP, et al.. 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, et al.. Pathway connectivity and signaling coordination in the yeast stress-activated signaling network. Molecular Systems Biology. 2014;10.
Honarpour N, Rose CM, Brumbaugh J, Anderson J, Graham RLJ, Sweredoski MJ, et al.. 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.
Hebert AS, Richards AL, Bailey DJ, Ulbrich A, Coughlin EE, Westphall MS, et al.. The One Hour Yeast Proteome. Molecular & Cellular Proteomics. 2014;13:339-347.
Dingley SD, Polyak E, Ostrovsky J, Srinivasan S, Lee I, Rosenfeld AB, 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.
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.
Keating DH, Zhang YP, Ong IM, McIlwain S, Morales EH, Grass JA, 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.
Rahimi A, Ulbrich A, Coon JJ, Stahl SS. Formic-acid-induced depolymerization of oxidized lignin to aromatics. Nature. 2014;515:249-52.
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.
Wenger CD, Coon JJ. A Proteomics Search Algorithm Specifically Designed for High-Resolution Tandem Mass Spectra. Journal of Proteome Research. 2013;12:1377-1386.
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.
Vincent CE, Potts GK, Ulbrich A, Westphall MS, Atwood JA, Coon JJ, et al.. Segmentation of Precursor Mass Range Using "Tiling" Approach Increases Peptide Identifications for MS1-Based Label-Free Quantification. Analytical Chemistry. 2013;85:2825-2832.
Still AJ, Floyd BJ, Hebert AS, Bingman CA, Carson JJ, Gunderson DR, et al.. Quantification of Mitochondrial Acetylation Dynamics Highlights Prominent Sites of Metabolic Regulation. Journal of Biological Chemistry. 2013;288:26209-26219.
Russell JD, Scalf M, Book AJ, Ladror DT, Vierstra RD, Smith LM, et al.. 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.
Rose CM, Russell JD, Ledvina AR, McAlister GC, Westphall MS, Griep-Raming J, et al.. 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.
Richards AL, Vincent CE, Guthals A, Rose CM, Westphall MS, Bandeira N, et al.. Neutron-encoded Signatures Enable Product Ion Annotation From Tandem Mass Spectra. Molecular & Cellular Proteomics. 2013;12:3812-3823.
Moussavi-Harami SF, Annis DS, Ma WJ, Berry SM, Coughlin EE, Strotman LN, 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.
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.
Ledvina AR, Rose CM, McAlister GC, Syka JEP, Westphall MS, Griep-Raming J, et al.. 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.
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.
Hebert AS, Merrill AE, Stefely JA, Bailey DJ, Wenger CD, Westphall MS, et al.. Amine-reactive Neutron-encoded Labels for Highly Plexed Proteomic Quantitation. Molecular & Cellular Proteomics. 2013;12:3360-3369.
Hebert AS, Merrill AE, Bailey DJ, Still AJ, Westphall MS, Strieter ER, et al.. Neutron-encoded mass signatures for multiplexed proteome quantification. Nature Methods. 2013;10:332-+.
Hebert AS, Dittenhafer-Reed KE, Yu W, Bailey DJ, Selen ES, Boersma MD, et al.. Calorie Restriction and SIRT3 Trigger Global Reprogramming of the Mitochondrial Protein Acetylome. Molecular Cell. 2013;49:186-199.
Frey BL, Ladror DT, Sondalle SB, Krusemark CJ, Jue AL, Coon JJ, et al.. Chemical Derivatization of Peptide Carboxyl Groups for Highly Efficient Electron Transfer Dissociation. Journal of the American Society for Mass Spectrometry. 2013;24:1710-1721.
Volkening JD, Bailey DJ, Rose CM, Grimsrud PA, Howes-Podoll M, Venkateshwaran M, et al.. A Proteogenomic Survey of the Medicago truncatula Genome. Molecular & Cellular Proteomics. 2012;11:933-944.
Van Etten J, Schagat TL, Hrit J, Weidmann CA, Brumbaugh J, Coon JJ, et al.. Human Pumilio Proteins Recruit Multiple Deadenylases to Efficiently Repress Messenger RNAs. Journal of Biological Chemistry. 2012;287:36370-36383.
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.
Rose CM, Venkateshwaran M, Volkening JD, Grimsrud PA, Maeda J, Bailey DJ, et al.. Rapid Phosphoproteomic and Transcriptomic Changes in the Rhizobia-legume Symbiosis. Molecular & Cellular Proteomics. 2012;11:724-744.
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.
McAlister GC, Russell JD, Rumachik NG, Hebert AS, Syka JEP, Geer LY, et al.. Analysis of the Acidic Proteome with Negative Electron-Transfer Dissociation Mass Spectrometry. Analytical Chemistry. 2012;84:2875-2882.
Ledvina AR, Lee MV, McAlister GC, Westphall MS, Coon JJ. Infrared Multiphoton Dissociation for Quantitative Shotgun Proteomics. Analytical Chemistry. 2012;84:4513-4519.
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.
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.
Brumbaugh J, Hou ZG, Russell JD, Howden SE, Yu PZ, Ledvina AR, et al.. Phosphorylation regulates human OCT4. Proceedings of the National Academy of Sciences of the United States of America. 2012;109:7162-7168.
Bailey DJ, Rose CM, McAlister GC, Brumbaugh J, Yu PZ, Wenger CD, et al.. 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.
Yang C, Park AC, Davis NA, Russell JD, Kim B, Brand DD, 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.
Xia Q, Lee VM, Rose CM, Marsh AJ, Hubler SL, Wenger CD, et al.. 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.
Wenger CD, Lee VM, Hebert AS, McAlister GC, Phanstiel DH, Westphall MS, et al.. Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging. Nature Methods. 2011;8:933-935.
Vasicek LA, Ledvina AR, Shaw J, Griep-Raming J, Westphall MS, Coon JJ, et al.. Implementing Photodissociation in an Orbitrap Mass Spectrometer. Journal of the American Society for Mass Spectrometry. 2011;22:1105-1108.
Russell JD, Hilger RT, Ladror DT, Tervo MA, Scalf M, Shortreed MR, et al.. 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, et al.. Proteomic and phosphoproteomic comparison of human ES and iPS cells. Nature Methods. 2011;8:821-U84.
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.
Lee VM, Topper SE, Hubler SL, Hose J, Wenger CD, Coon JJ, et al.. A dynamic model of proteome changes reveals new roles for transcript alteration in yeast. Molecular Systems Biology. 2011;7 514 514.
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.
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.
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.
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.
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.
Ledvina AR, Beauchene NA, McAlister GC, Syka JEP, Schwartz JC, Griep-Raming J, et al.. 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.
Grimsrud PA, Swaney DL, Wenger CD, Beauchene NA, Coon JJ. Phosphoproteomics for the Masses. ACS Chemical Biology. 2010;5:105-119.
Good DM, Zuerbig P, Argiles A, Bauer HW, Behrens G, Coon JJ, et al.. Naturally Occurring Human Urinary Peptides for Use in Diagnosis of Chronic Kidney Disease. Molecular & Cellular Proteomics. 2010;9:2424-2437.
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.
Good DM, Coon JJ. Mass Spectrometric Analysis of Body Fluids for Biomarker Discovery. In: Ottens AK, Wang KKW. 2009. pp. 277-291.
Swaney DL, Wenger CD, Thomson JA, Coon JJ. Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America. 2009;106:995-1000.
Second TP, Blethrow JD, Schwartz JC, Merrihew GE, MacCoss MJ, Swaney DL, et al.. Dual-Pressure Linear Ion Trap Mass Spectrometer Improving the Analysis of Complex Protein Mixtures. Analytical Chemistry. 2009;81:7757-7765.
Sadygov RG, Good DM, Swaney DL, Coon JJ. A New Probabilistic Database Search Algorithm for ETD Spectra. Journal of Proteome Research. 2009;8:3198-3205.
Phanstiel D, Unwin R, McAlister GC, Coon JJ. Peptide Quantification Using 8-Plex Isobaric Tags and Electron Transfer Dissociation Tandem Mass Spectrometry. Analytical Chemistry. 2009;81:1693-1698.
Mischak H, Coon JJ, Novak J, Weissinger EM, Schanstra JP, Dominiczak AF. Capillary Electrophoresis-Mass Spectrometry as a Powerful Tool in Biomarker Discovery and Clinical Diagnosis: An Update of Recent Developments. Mass Spectrometry Reviews. 2009;28:703-724.
McGivern JV, Swaney DL, Coon JJ, Sheets MD. Toward Defining the Phosphoproteome of Xenopus laevis Embryos. Developmental Dynamics. 2009;238:1433-1443.
Madsen JA, Gardner MW, Smith SI, Ledvina AR, Coon JJ, Schwartz JC, et al.. Top-Down Protein Fragmentation by Infrared Multiphoton Dissociation in a Dual Pressure Linear Ion Trap. Analytical Chemistry. 2009;81:8677-8686.
Ledvina AR, McAlister GC, Gardner MW, Smith SI, Madsen JA, Schwartz JC, et al.. Infrared Photoactivation Reduces Peptide Folding and Hydrogen-Atom Migration following ETD Tandem Mass Spectrometry. Angewandte Chemie-International Edition. 2009;48:8526-8528.
Haubitz M, Good DM, Woywodt A, Haller H, Rupprecht H, Theodorescu D, et al.. Identification and Validation of Urinary Biomarkers for Differential Diagnosis and Evaluation of Therapeutic Intervention in Anti-neutrophil Cytoplasmic Antibody-associated Vasculitis. Molecular & Cellular Proteomics. 2009;8:2296-2307.
Good DM, Wenger CD, McAlister GC, Bai DL, Hunt DF, Coon JJ. Post-Acquisition ETD Spectral Processing for Increased Peptide Identifications. Journal of the American Society for Mass Spectrometry. 2009;20:1435-1440.
Gardner MW, Smith SI, Ledvina AR, Madsen JA, Coon JJ, Schwartz JC, et al.. Infrared Multiphoton Dissociation of Peptide Cations in a Dual Pressure Linear Ion Trap Mass Spectrometer. Analytical Chemistry. 2009;81:8109-8118.
Duellman SJ, Thompson KL, Coon JJ, Burgess RR. Phosphorylation sites of Epstein-Barr virus EBNA1 regulate its function. Journal of General Virology. 2009;90:2251-2259.
Coon JJ. Collisions or Electrons? Protein Sequence Analysis in the 21st Century. Analytical Chemistry. 2009;81:3208-3215.
Zurbig P, Decramer S, Dakna M, Jantos J, Good DM, Coon JJ, et al.. The human urinary proteome reveals high similarity between kidney aging and chronic kidney disease. Proteomics. 2009;9:2108-2117.
Zimmerli LU, Schiffer E, Zuerbig P, Good DM, Kellmann M, Mouls L, et al.. Urinary proteomic biomarkers on coronary artery disease. Molecular & Cellular Proteomics. 2008;7:290-298.
Theodorescu D, Schiffer E, Bauer HW, Douwes F, Eichhorn F, Polley R, et al.. Discovery and validation of urinary biomarkers for propstate cancer. Proteomics Clinical Applications. 2008;2:556-570.
Swaney DL, McAlister GC, Coon JJ. Decision tree-driven tandem mass spectrometry for shotgun proteomics. Nature Methods. 2008;5:959-964.
Rossing K, Mischak H, Dakna M, Zuerbig P, Novak J, Julian BA, et al.. Urinary proteomics in diabetes and CKD. Journal of the American Society of Nephrology. 2008;19:1283-1290.
Phanstiel D, Zhang Y, Marto JA, Coon JJ. Peptide and protein quantification using iTRAQ with electron transfer dissociation. Journal of the American Society for Mass Spectrometry. 2008;19:1255-1262.
Phanstiel D, Brumbaugh J, Berggren TW, Conard K, Feng X, Levenstein ME, et al.. Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells. Proceedings of the National Academy of Sciences of the United States of America. 2008;105:4093-4098.
McAlister GC, Kiessel SEB, Coon JJ. In vacuo formation of peptide-metal coordination complexes. International Journal of Mass Spectrometry. 2008;276:149-152.
McAlister GC, Berggren TW, Griep-Raming J, Horning S, Makarov A, Phanstiel D, et al.. A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer. Journal of Proteome Research. 2008;7:3127-3136.
Hubler SL, Jue A, Keith J, McAlister GC, Craciun G, Coon JJ. Valence parity renders z(center dot)-type ions chemically distinct. Journal of the American Chemical Society. 2008;130:6388-6394.
Frey BL, Krusemark CJ, Ledvina AR, Coon JJ, Belshaw PJ, Smith LM. Ion-ion reactions with fixed-charge modified proteins to produce ions in a single, very high charge state. International Journal of Mass Spectrometry. 2008;276:136-143.
Coon JJ, Zuerbig P, Dakna M, Dominicza AF, Decramer S, Fliser D, et al.. CE-MS analysis of the human urinary proteome for biomarker discovery and disease diagnostics. Proteomics Clinical Applications. 2008;2:964-973.
Brumbaugh J, Phanstiel D, Coon JJ. Unraveling the histone's potential A proteomics perspective. Epigenetics. 2008;3:254-257.
Swaney DL, McAlister GC, Wirtala M, Schwartz JC, Syka JEP, Coon JJ. Supplemental activation method for high-efficiency electron-transfer dissociation of doubly protonated peptide precursors. Analytical Chemistry. 2007;79:477-485.
Swaney DL, McAlister GC, Phanstiel D, Brumbaugh J, Keith J, Ficarro SB, et al.. New technology to detect and monitor the post-translational modification events that commit human embryonic stem cells to exit the pluripotent state. Molecular & Cellular Proteomics. 2007;6:36-36.
McAlister GC, Phanstiel D, Good DM, Berggren TW, Coon JJ. Implementation of electron-transfer dissociation on a hybrid linear ion trap-orbitrap mass spectrometer. Analytical Chemistry. 2007;79:3525-3534.
Lecchi S, Nelson CJ, Allen KE, Swaney DL, Thompson KL, Coon JJ, et al.. Tandem phosphorylation of Ser-911 and Thr-912 at the C terminus of yeast plasma membrane H+-ATPase leads to glucose-dependent activation. Journal of Biological Chemistry. 2007;282:35471-35481.
Khidekel N, Ficarro SB, Clark PM, Bryan MC, Swaney DL, Rexach JE, et al.. Probing the dynamics of O-GlcNAc glycosylation in the brain using quantitative proteomics. Nature Chemical Biology. 2007;3:339-348.
Julian BA, Wittke S, Novak J, Good DM, Coon JJ, Kellmann M, et al.. Electrophoretic methods for analysis of urinary polypeptides in IgA-associated renal diseases. Electrophoresis. 2007;28:4469-4483.
Good DM, Wirtala M, McAlister GC, Coon JJ. Performance characteristics of electron transfer dissociation mass spectrometry. Molecular & Cellular Proteomics. 2007;6:1942-1951.
Good DM, Thongboonkerd V, Novak J, Bascands J-L, Schanstra JP, Coon JJ, et al.. Body fluid proteomics for biomarker discovery: Lessons from the past hold the key to success in the future. Journal of Proteome Research. 2007;6:4549-4555.
Williams DK, McAlister GC, Good DM, Coon JJ, Muddiman DC. Dual electrospray ion source for electron-transfer dissociation on a hybrid linear ion trap-orbitrap mass spectrometer. Analytical Chemistry. 2007;79:7916-7919.
Chi A, Huttenhower C, Geer LY, Coon JJ, Syka JEP, Bai DL, et al.. Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America. 2007;104:2193-2198.
Mikesh LM, Ueberheide B, Chi A, Coon JJ, Syka JEP, Shabanowitz J, et al.. The utility of ETD mass spectrometry in proteomic analysis. Biochimica Et Biophysica Acta-Proteins and Proteomics. 2006;1764:1811-1822.
Good DM, Coon JJ. Advancing proteomics with ion/ion chemistry. BioTechniques. 2006;40:783.
Yue GE, Roper MG, Balchunas C, Pulsipher A, Coon JJ, Shabanowitz J, et al.. Protein digestion and phosphopeptide enrichment on a glass microchip. Analytica Chimica Acta. 2006;564:116-122.
Coon JJ, Ueberheide B, Syka JEP, Dryhurst DD, Ausio J, Shabanowitz J, et al.. Protein identification using sequential ion/ion reactions and tandem mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America. 2005;102:9463-9468.
Coon JJ, Syka JEP, Shabanowitz J, Hunt DF. Tandem mass spectrometry for peptide and protein sequence analysis. BioTechniques. 2005;38:519-+.
Coon JJ, Shabanowitz J, Hunt DF, Syka JEP. Electron transfer dissociation of peptide anions. Journal of the American Society for Mass Spectrometry. 2005;16:880-882.
Syka JEP, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America. 2004;101:9528-9533.
Schroeder MJ, Shabanowitz J, Schwartz JC, Hunt DF, Coon JJ. A neutral loss activation method for improved phosphopeptide sequence analysis by quadrupole ion trap mass spectrometry. Analytical Chemistry. 2004;76:3590-3598.
Coon JJ, Syka JEP, Schwartz JC, Shabanowitz J, Hunt DF. Anion dependence in the partitioning between proton and electron transfer in ion/ion reactions. International Journal of Mass Spectrometry. 2004;236:33-42.
Coon JJ, Steele HA, Laipis PJ, Harrison WW. Direct atmospheric pressure coupling of polyacrylamide gel electrophoresis to mass spectrometry for rapid protein sequence analysis. Journal of Proteome Research. 2003;2:610-617.
Coon JJ, Steele HA, Laipis PJ, Harrison WW. Laser desorption-atmospheric pressure chemical ionization: a novel ion source for the direct coupling of polyacrylamide gel electrophoresis to mass spectrometry. Journal of Mass Spectrometry. 2002;37:1163-1167.
Coon JJ, McHale KJ, Harrison WW. Atmospheric pressure laser desorption/chemical ionization mass spectrometry: a new ionization method based on existing themes. Rapid Communications in Mass Spectrometry. 2002;16:681-685.
Coon JJ, Harrison WW. Laser desorption-atmospheric pressure chemical ionization mass spectrometry for the analysis of peptides from aqueous solutions. Analytical Chemistry. 2002;74:5600-5605.