All Faculty and Research Staff Publications

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2008
Jorabchi K, Westphall MS, Smith LM. Charge assisted laser desorption/ionization mass spectrometry of droplets. Journal of the American Society for Mass Spectrometry. 2008 ;19:833-840.
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.
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.
Volkening JD, Bailey DJ, Rose CM, Grimsrud PA, Howes-Podoll M, Venkateshwaran M, Westphall MS, Ane JM, Coon JJ, Sussman MR. A Proteogenomic Survey of the Medicago truncatula Genome. Molecular & Cellular Proteomics. 2012 ;11:933-944.
Grimsrud PA, Carson JJ, Hebert AS, Hubler SL, Niemi NM, Bailey DJ, Jochem A, Stapleton DS, Keller MP, Westphall MS, et al. A Quantitative Map of the Liver Mitochondrial Phosphoproteome Reveals Posttranslational Control of Ketogenesis. Cell Metabolism. 2012 ;16:672-683.
Rose CM, Venkateshwaran M, Volkening JD, Grimsrud PA, Maeda J, Bailey DJ, Park K, Howes-Podoll M, D. Os den, Yeun LH, et al. Rapid Phosphoproteomic and Transcriptomic Changes in the Rhizobia-legume Symbiosis. Molecular & Cellular Proteomics. 2012 ;11:724-744.
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.
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.
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.
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.

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