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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. |
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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. |
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Mednikov EG, Dahl LF, Peterson AC, Russell JD, Bailey DJ, Westphall MS, et al. How innocent is thallium(I)? Corrected formulations of Tl2Pd14(CO)(9)(PMe3)(11) PF6 (2) and TlPd9(CO)(9)(PPh3)(6) PF6 clusters previously reported as corresponding Au2Pd14 and AuPd9 clustersParallel Reaction Monitoring for High Resolution and High Mass Ac. Chemical Communications. 2013;49:1085-1087. |
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Tainter CJ, Ni Y, Shi L, Skinner JL, Mednikov EG, Dahl LF, et al. Hydrogen Bonding and OH-Stretch Spectroscopy in Water: Hexamer (Cage), Liquid Surface, Liquid, and IceHow innocent is thallium(I)? Corrected formulations of Tl2Pd14(CO)(9)(PMe3)(11) PF6 (2) and TlPd9(CO)(9)(PPh3)(6) PF6 clusters previously reported as cor. Journal of Physical Chemistry Letters. 2013;4:12-17. |
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Tan YZ, Jin S, Hamers RJ, Tainter CJ, Ni Y, Shi L, et al. Influence of Hole-Sequestering Ligands on the Photostability of CdSe Quantum DotsHydrogen Bonding and OH-Stretch Spectroscopy in Water: Hexamer (Cage), Liquid Surface, Liquid, and IceHow innocent is thallium(I)? Corrected formulations of Tl2Pd14(CO)(9)(PM. Journal of Physical Chemistry C. 2013;117:313-320. |
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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. |
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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. |
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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. |
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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. |
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Ledvina AR, Lee MV, McAlister GC, Westphall MS, Coon JJ. Infrared Multiphoton Dissociation for Quantitative Shotgun Proteomics. Analytical Chemistry. 2012;84:4513-4519. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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Grimsrud PA, Swaney DL, Wenger CD, Beauchene NA, Coon JJ. Phosphoproteomics for the Masses. ACS Chemical Biology. 2010;5:105-119. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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Grimsrud PA, den Os D, Wenger CD, Swaney DL, Schwartz D, Sussman MR, et al. Large-scale phosphoprotein analysis in Medicago truncatula roots provides insight into in vivo kinase activity in legumes. Plant Physiol. 2010;152(1):19-28. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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McGivern JV, Swaney DL, Coon JJ, Sheets MD. Toward Defining the Phosphoproteome of Xenopus laevis Embryos. Developmental Dynamics. 2009;238:1433-1443. |
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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. |
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Phanstiel D, Brumbaugh J, McAlister GC, Wenger CD, Stewart R, Tian S, et al. New Technology for the Large-scale Proteomic Comparison of Human Embryonic Stem Cells, Induced Pluripotent Stem Cells, and Somatic Cells. Molecular & Cellular Proteomics. 2009;:S11-S11. |
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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. |
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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. |
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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. |
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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. |
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Zürbig 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(8):2108-17. |
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Coon JJ. Collisions or electrons? Protein sequence analysis in the 21st century. Anal Chem. 2009;81(9):3208-15. |
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Good DM, Coon JJ. Mass spectrometric analysis of body fluids for biomarker discovery. Methods Mol Biol. 2009;566:277-91. |
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Brumbaugh J, Phanstiel D, Coon JJ. Unraveling the histone's potential A proteomics perspective. Epigenetics. 2008;3:254-257. |
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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. |
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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. |
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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. |
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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. |
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McAlister GC, Kiessel SEB, Coon JJ. In vacuo formation of peptide-metal coordination complexes. International Journal of Mass Spectrometry. 2008;276:149-152. |
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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. |
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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. |
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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. |
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Swaney DL, McAlister GC, Coon JJ. Decision tree-driven tandem mass spectrometry for shotgun proteomics. Nature Methods. 2008;5:959-964. |
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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. |
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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. |
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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. |
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Good DM, Wirtala M, McAlister GC, Coon JJ. Performance characteristics of electron transfer dissociation mass spectrometry. Molecular & Cellular Proteomics. 2007;6:1942-1951. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. Proc Natl Acad Sci U S A. 2007;104(7):2193-8. |
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Williams KD, 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. Anal Chem. 2007;79(20):7916-9. |
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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(23):4469-83. |
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Good DM, Coon JJ. Advancing proteomics with ion/ion chemistry. BioTechniques. 2006;40:783. |
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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. |
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Yue GE, Roper MG, Balchunas C, Pulsipher A, Coon JJ, Shabanowitz J, et al. Protein digestion and phosphopeptide enrichment on a glass microchip. Anal Chim Acta. 2006;564(1):116-22. |
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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. |
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Coon JJ, Syka JEP, Shabanowitz J, Hunt DF. Tandem mass spectrometry for peptide and protein sequence analysis. BioTechniques. 2005;38:519-+. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
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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. |
