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172.	Shi, H.; Pierson, N.; Valentine, S.; Clemmer,D.E. Conformation Types of Ubiquitin [M+8H]⁸⁺ Ions from Water: Methanol Solutions: Evidence for the N and A States in Aqueous Solution (Journal of Physical Chemistry, November 2011)

Published

171.	Isailovic, D.; Plasencia, M.; Gaye, M.; Stokes, S.; Kurulugama, R.; Pungpapong, V.; Zhang, M.; Kyselova, Z.; Goldman, R.; Mechref, Y.; Novotny, M.V.; Clemmer, D.E. Delineating Diseases by IMS-MS Profiling of Serum N-linked Glycans (J. Proteome Res., Article ASAP, DOI: 10.1021/pr200777u, Publication Date (Web): December 12, 2011)
170.	Lee, S.; Valentine, S.J.; Reilly, J.P.; Clemmer, D.E. Analyzing a Mixture of Disaccharides by IMS-VUVPD-MS. International Journal of Mass Spectrometry, 2012, 309, 161–167.
169.	Lee, S.; Valentine, S.J.; Zucker, S.M.; Webber, N.; Reilly, J.P.; Clemmer, D.E. Extracted Fragment Ion Mobility Distributions: A New Method for Complex Mixture Analysis. International Journal of Mass Spectrometry, 2012, 309, 154-160.
168.	Lee, S.; Valentine, S.J.; Reilly, J.P.; and Clemmer, D.E. Controlled Formation of Peptide Bonds in the Gas-Phase. J. Am. Chem. Soc.,2011,133(40), 15834–15837.
167.	Kurulugama, R.T.; Nachtigall, F. M.; Valentine, S. J.; Clemmer, D.E. Overtone Mobility Spectrometry: Part 4. OMS-OMS Analyses of Complex Mixtures. J. Am. Soc. Mass Spectrom. 2011, Volume 22, 2049-2060.
166.	Zucker, S.M.; Lee, S.; Webber, N.; Valentine, S.J.; Reilly, J.P. and Clemmer, D.E. An Ion Mobility/Ion Trap/Photodissociation Instrument for Characterization of Ion Structure. J. Am. Soc. Mass Spectrom., 2011, 22(9), 1477-1485.
165.	Bohrer, B.C. and Clemmer, D.E. Shift Reagents for Multidimensional Ion Mobility Spectrometry-Mass Spectrometry Analysis of Complex Peptide Mixtures: Evaluation of 18-Crown-6 Ether Complexes . Analytical Chemistry, 2011, 83 (13), 5377–5385.
164.	Bohrer, B.C. and Clemmer, D.E. Biologically-Inspired Peptide Reagents for Enhancing IMS-MS Analysis of Carbohydrates. J. Am. Soc. Mass Spectrom., 2011, 22(9), 1602-1609.
163.	Pierson, N.A.; Chen, L., Valentine, S.J.; Russell, D.H.; Clemmer, D.E. Number of Solution States of Bradykinin from Ion Mobility and Mass Spectrometry Measurements. J. Am. Chem. Soc., 2011, 133 (35), 13810–13813.
162.	Jung, J.E.; Pierson, N.A.; Marquardt, A.; Scheffner, M.; Przybylski, M., Clemmer, D.E. Differentiation of Compact and Extended Conformations of Di-Ubiquitin Conjugates with Lysine-Specific Isopeptide Linkages Revealed by Ion Mobility Mass Spectrometry, J. Am. Soc. Mass Spectrom. 2011, 22, 1463-1471.
161.	Valentine, S.J.; Ewing, M.; Dilger, J.M.; Glover, M.; Geromanos, S.; Hughes, C.; Clemmer, D.E. Using Ion Mobility Data to Improve Peptide Identification: Cross Section Databases and Intrinsic Amino Acid Size Parameters. J. Proteome Res., 2011, 10 (5), 2318–2329.
160.	Valentine, S.J.; Kurulugama, R.T.; Clemmer, D. E. Overtone Mobility Spectrometry: Part 3. On the Origin of Peaks. J Am Soc Mass Spectrom. 2011, 22(5), 804-16.
159.	Li, Z.; Valentine, S.J.; Clemmer, D.E. Complexation of Amino Compounds by 18C6 Improves Selectivity by IMS-IMS-MS: Application to Petroleum Characterization. J Am Soc Mass Spectrom. 2011, 22(5), 817-27.
158.	Bohrer, B.; Atlasevich, N.; Clemmer, D.E. Transitions between Elongated Conformations of Ubiquitin [M+11H]¹¹⁺ Enhance Hydrogen/Deuterium Exchange. J. Phys. Chem. B 2011, 115 (15), 4509–4515.
157.	Bohrer, Brian C.; Li, Yong Fuga; Reilly, James P.; Clemmer, David E.; Di Marchi, Richard D.; Radivojac, Predrag; Tang, Haixu; Arnold, Randy J. Combinatorial Libraries of Synthetic Peptides as a Model for Shotgun Proteomics. Analytical Chemistry 2010, 82(15), 6559-6568.
156.	Kim, Tae-Young; Valentine, Stephen J.; Clemmer, David E.; Reilly, James P. Gas-Phase Conformation-Specific Photofragmentation of Proline-Containing Peptide Ions. Journal of the American Society for Mass Spectrometry 2010, 21(8), 1455-1465.
155.	Trimpin, S., Clemmer, D.E., and Larsen, B.S. Snapshot, Conformation, and Bulk Fragmentation of Polymeric Architectures using ESI-IMS-MS, Ion Mobility Spectrometry: Theory and Applications, Taylor and Francis Group, 2010. (Book Chapter)
154.	Glaskin, Rebecca S.; Valentine, Stephen J.; Clemmer, David E. A Scanning Frequency Mode for Ion Cyclotron Mobility Spectrometry. Analytical Chemistry 2010, 82(19), 8266-8271.
153.	Shvartsburg, Alexandre A.; Clemmer, David E.; Smith, Richard D. Isotopic Effect on Ion Mobility and Separation of Isotopomers by High-Field Ion Mobility Spectrometry. Analytical Chemistry 2010, 82(19), 8047-8051.
152.	Lee, Sunyoung; Ewing, Michael A.; Nachtigall, Fabiane M.; Kurulugama, Ruwan T.; Valentine, Stephen J.; Clemmer, David E. Determination of Cross Sections by Overtone Mobility Spectrometry: Evidence for Loss of Unstable Structures at Higher Overtones. Journal of Physical Chemistry B 2010, 114(38), 12406-12415.
151.	Robinson, Rena A. S.; Kellie, John F.; Kaufman, Thomas C.; Clemmer, David E. Insights into aging through measurements of the Drosophila proteome as a function of temperature. Mechanisms of Ageing and Development 2010, 131(9), 584-590.
150.	[Note, 150 is an erratum] Plasencia, M. D.; Isailovic, D.; Merenbloom, S. I.; Mechref, Y.; Novotny, M. V.; Clemmer, D. E. Resolving and Assigning N-linked Glycan Structural Isomers from Ovalbumin by IMS-MS. J. Am. Soc. Mass Spectrom. 21(1) 2010, 191 [original: 19(11), 2008, 1706-1715]
149.	Pierson, Nicholas; Valentine, Stephen; Clemmer, David. Evidence for a Quasi-Equilibrium Distribution of States for Bradykinin [M+3H]3+ Ions in the Gas Phase. J. Phys. Chem. B, 2010, 114, 7777–7783
148.	Liu, X., Afrane, M., Clemmer, D.E., Zhong, G., Nelson, D.E. Identification of Chlamydia trachomatis outer membrane complex proteins by differential proteomics. J Bacteriol. 2010, 192(11), 2852-2860
147.	Xun, Z., Kaufman, T.C., Clemmer, D.E. Stable Isotope labeling and label-free proteomics of Drosophila parkin null mutants . J. Proteome Research, 2009, 8(10), 4500-4510.
146.	Valentine, S. J.; Clemmer, D. E. Protein oligomers frozen in time. Nature Chemistry 2009, 1 (4), 257-258.
145.	Valentine, S. J.; Clemmer, D. E. Treatise on the Measurement of Molecular Masses with Ion Mobility Spectrometry Analytical Chemistry 2009, 81(14), 5876-5880
144.	Trimpin, S., Tan, B., Bohrer, B.C., O’Dell, D.K., Merenbloom, S.I., Pazos, M.X., Clemmer, D.E., Walker, J.M. Profiling of Phospholipids and Related Lipid Structures using Multidimensional Ion Mobility Spectrometry-Mass Spectrometry. International Journal of Mass Spectrometry 2009, 287, 58-69.
143.	Valentine, S. J.; Kurulugama, R. T.; Bohrer, B. C.; Merenbloom, S. I.; Sowell, R. A.; Mechref, Y; Clemmer, D. E. Developing IMS–IMS–MS for rapid characterization of abundant proteins in human plasma. International Journal of Mass Spectrometry 2009, 283, 149–160.
142.	Merenbloom, Samuel I.; Glaskin, Rebecca S.; Henson, Zachary B.; Clemmer, David E. High-Resolution Ion Cyclotron Mobility Spectrometry. Analytical Chemistry 2009, 81(4), 1482-1487.
141.	Valentine, S.J., Stokes, S.T. Kurulugama, R., Nachtigall, F.M., Clemmer, D.E. Overtone Mobility Spectrometry (Part2): Theoretical Considerations of Resolving Power. J. Am. Soc. Mass Spectrom. 2009, 20 (5), 738-750.
140.	Kurulugama, R., Nachtigall, F.M., Lee, S., Valentine, S.J., Clemmer, D.E. Overtone Mobility Spectrometry (Part1): Experimental Observations J. Am. Soc. Mass Spectrom. 2009, 20 (5), 729-737.
139.	Xun, Z.; Kaufman, T. C.; Clemmer, D. E. Proteome response to the panneural expression of human wild-Type -Synuclein: a Drosophila Model of Parkinson’s Disease. J. Proteome Res. 2008, 7, 3911-3921
138.	Trimpin, Sarah; Clemmer, David E. Ion Mobility Spectrometry/Mass Spectrometry Snapshots for Assessing the Molecular Compositions of Complex Polymeric Systems. Analytical Chemistry 2008 80 (23), 9073-9083.
137.	Plasencia, M. D. ; Isailovic, D. ; Merenbloom, S. I. ; Mechref, Y. ; Clemmer, D. E. Resolving and Assigning N-linked Glycan Structural Isomers from Ovalbumin by IMS-MS. J. Am. Soc. Mass Spectrom. 2008, 19(11), 1706-1715.
136.	Kurulugama, R. T.; Valentine, S. J.; Sowell, R. A.; Clemmer, D. E. Development of a high-throughput IMS-IMS-MS approach for analyzing mixtures of biomolecules. J. Proteomics, 2008, 71(3), 318-331.
135.	Xun, Z.; Sowell, R. A.; Kaufman, T. C.; Clemmer, D. E. Quantitative Proteomics of a Presymptomatic A53T -Synuclein* Drosophila Model of Parkinson Disease.* Mol. Cell. Proteomics, 2008, 7, 1191-1203.
134.	Alves, P. ; Arnold, R. J. ; Clemmer, D. E. ; Li, Y. ; Reilly, J. P. ; Sheng, Q. ; Tang, H. ; Xun, Z. ; Zeng, R. ; Radivojac, P. Fast and accurate identification of semi-tryptic peptides in shotgun proteomics. Bioinformatics 2008, 24(1), 102-109.
133.	Merenbloom, S. I. ; Koeniger, S. L. ; Bohrer, B. C. ; Valentine, S. J. ; Clemmer, D. E. Improving the Efficiency of IMS-IMS by a Combing Technique. Analytical Chemistry 2008, 80(6), 1918-1927.
132.	Polfer, N. C.; Bohrer, B. C.; Plasencia, M. D.; Paizs, B.; Clemmer, D. E. On the dynamics of primary structure scrambling in collision-induced dissociation of peptides J. Phys Chem. A 2008, 112, 1286-1293.
131.	Isailovic, D. ; Kurulugama, R. T. ; Plasencia, M. D. ; Stokes, S. T. ; Kyselova, Z. ; Goldman, R. ; Mechref, Y. ; Novotny, M. V. ; Clemmer, D. E. Profiling of Human Serum Glycans Associated with Liver Cancer and Cirrhosis by IMS-MS. J. Proteome Res. 2008, 7(3), 1109-1117.
130.	Bohrer, B. C. ; Merenbloom, S. I. ; Koeniger, S. L. ; Hilderbrand, A. E. ; Clemmer, D. E. Biomolecule Analysis by Ion Mobility Spectrometry, Annu. Rev. Analytical Chemistry 2008, 1, 10. 1-10. 35
129.	Trimpin, S.; Clemmer, D. E.; McEwen, C. N. Charge-remote fragmentation of lithiated fatty acids on a TOF-TOF instrument J. Am. Soc. Mass. Spectrom. 2007, 18, 1967-1972.
128.	Sowell, R. A., Hersberger, K. E., Kaufman, T. C., Clemmer, D. E. Examining the Proteome of Drosophila across Organism Lifespan J. Proteome Res. 2007, 6, 3637-3647.
127.	Xun, Z.; Sowell, R. A.; Kaufman, T. C.; Clemmer, D. E. Lifetime Proteomic Profiling of an A30P α-synuclein Drosophila Model of Parkinson's Disease J. Proteome Res. 2007, 6, 3729-3738.
126.	Liu, X.; Miller, B. R.; Rebec, G. V.; Clemmer, D. E. Protein Expression in the Striatum and Cortex Regions of the Brain for a Mouse Model of Huntington's Disease J. Proteome Res. 2007, 6, 3134-3142.
125.	Liu, X.; Valentine, S. J.; Plasencia, M. D.; Trimpin, S.; Naylor, S.; Clemmer, D. E. Mapping the Human Plasma Proteome by SCX-LC-IMS-MS. J. Am. Soc. Mass Spectrom. 2007, 18, 1249-1264. (cover image)
124.	Trimpin, S.; Plasencia, M.; Isailovic, D.; Clemmer, D. E. Resolving Oligomers from Fully Grown Polymers with IMS-MS Analytical Chemistry 2007, 79, 7965-7974.
123.	Xun, Z.; Sowell, R. A.; Kaufman, T. C.; Clemmer, D. E. Protein Expression in a Drosophila Model of Parkinson's Disease, J. Proteome Research 2007, 6, 348-357.
122.	Merenbloom, S. I.; Bohrer, B. C.; Koeniger, S. L.; Clemmer, D. E. Assessing the Peak Capacity of IMS-IMS Separations of Tryptic Peptide Ions in 300 K He. Analytical Chemistry 2007, 79, 515-522. (cover image)
121.	Koeniger, S. L.; Clemmer, D. E. Resolution and Structural Transitions of Elongated States of Ubiquitin. J. Am. Soc. Mass Spectrom. 2007, 18, 322-331.
120.	Myung, S.; Lorton, P.; Merenbloom, S. I.; Fioroni, M.; Koeniger, S. L.; Julian, R. R.; Baik, M-H.; Clemmer, D. E. Evidence for Spontaneous Resolution of Icosahedral Proline. J. Am. Chem. Soc. 2006 128, 15988-15989.
119.	Valentine, S. J.; Plasencia, M. D.; Liu, X.; Krishnan, M.; Naylor, S.; Udseth, H. R.; Smith, R. D.; Clemmer, D. E. Toward Plasma Proteome Profiling with Ion Mobility-Mass Spectrometry, J. Proteome Research 2006, 5, 2977-2984.
118.	Myung, S.; Fioroni, M.; Julian, R. R.; Koeniger, S. L.; Baik, M-H.; Clemmer, D. E. Chirally Directed Formation of Nanometer-Scale Proline Clusters, J. Am. Chem. Soc. 2006, 128, 10833-10839.
117.	Koeniger, S. L.; Merenbloom, S. I.; Sevugarajan, S.; Clemmer, D. E. Transfer of Structural Elements from Compact to Extended States in Unsolvated Ubiquitin, J. Am. Chem. Soc. 2006, 128, 11713-11719.
116.	Hilderbrand, A. E.; Myung, S.; Clemmer, D. E. Exploring Crown Ethers as Shift Reagents for Ion Mobility Spectrometry, Analytical Chemistry 2006, 78, 6792-6800.
115.	Tang, H.; Arnold, R. J.; Alves, P.; Xun, Z.; Clemmer, D. E.; Novotny, M. V.; Reilly, J. P.; Radivojac, P. A Computational Approach Toward Label-free Protein Quantification using Predicted Peptide Detectability, Bioinformatics 2006, 22, 481-488.
114.	Valentine, S. J.; Sevugarajan, S.; Kurulugama, R. T.; Koeniger, S. L.; Merenbloom, S. I.; Bohrer, B. C.; Clemmer, D. E. Split-Field Drift Tube/Mass Spectrometry and Isotopic Labeling Techniques for Determination of Single Amino Acid Polymorphisms, J. Proteome Research 2006, 5, 1879-1887.
113.	Koeniger, S. L.; Merenbloom, S. I.; Valentine, S. J.; Jarrold, M. F.; Udseth, H.; Smith, R.; Clemmer, D. E. An IMS-IMS Analogue of MS-MS, Analytical Chemistry 2006, 78, 4161-4174.
112.	Myung, S.; Valentine, S. J.; Clemmer, D. E. Ion-Mobility Spectrometry Combined with Mass Spectrometry: Principles and Applications in Protein Characterization in Encyclopedia of Mass Spectrometry (Hyphenated Methods , Volume 8), Gross, M. L.; Caprioli, R. and Niessen, W. M. A., Eds.; Elsevier: Kidlington, Oxford, 2006.
111.	Merenbloom, S. I.; Koeniger, S. L.; Valentine, S. J.; Plasencia, M. D.; Clemmer, D. E. IMS-IMS and IMS-IMS-IMS/MS for Separating Peptide and Protein Fragment Ions, Analytical Chemistry 2006, 78, 2802-2809.
110.	Koeniger, S. L.; Merenbloom, S. I.; Clemmer, D. E. Evidence for Many Resolvable Structures within Conformation Types of Electrosprayed Ubiquitin Ions, J. Phys. Chem B 2006, 110, 7017-7021.
109.	Myung, S.; Wiseman, J. M.; Valentine, S. J.; Zoltán, T. Cooks, R. G.; Clemmer, D. E. Coupling Desorption Electrospray Ionization (DESI) with Ion Mobility/Mass Spectrometry for Analysis of Protein Structure: Evidence for Desorption of Folded and Denatured States, J. Phys. Chem B 2006, 110, 5045-5051.
108.	Badman, E.; Myung, S.; Clemmer. D. E. Evidence for Unfolding and Refolding of Gas Phase Cyctrochrome c Ions in a Paul Trap, J. Am. Soc. Mass Spectrom. 2005, 16, 1493-1497.
107.	Taraszka, J. A.; Gao, X.; Valentine, S. J.; Sowell, R. A.; Koeniger, S. L; Miller, D. F.; Kaufman, T. C.; Clemmer, D. E. Proteome Profiling for Assessing Diversity: Analysis of Individual Heads of Drosophila melanogaster Using LC-Ion Mobility-MS, J. Proteome Research 2005, 4, 1238-1247.
106.	Taraszka, J. A.; Kurulugama, R.; Sowell, R.; Valentine, S. J.; Koeniger, S. L; Arnold, R. J.; Miller, D. F.; Kaufman, T. C.; Clemmer, D. E. Mapping the Proteome of Drosophila melanogaster: Analysis of Embryos and Adult Heads by LC-IMS-MS Methods, J. Proteome Research 2005, 4, 1223-1237.
105.	Valentine, S. J.; Liu, X.; Plasencia, M. D.; Hilderbrand, A. E.; Kurulugama, R. T.; Koeniger, S. L.; Clemmer, D. E. Developing liquid chromatography ion mobility mass spectrometry techniques, Expert Rev. Proteomics 2005, 2, 553-565.
104.	Myung, S.; Pink, M.; Baik, M.; Clemmer, D. E. DL-Proline, Acta Cryst. 2005, C61, 506-508.
103.	Wong, R. L.; Counterman, A. E.; Clemmer, D. E.; Williams, E. R. Evaluation of Ion Mobility Spectroscopy for Determining Charge-Solvated versus Salt-Bridge Structures of Protonated Trimers, J. Am. Soc. Mass Spectrom. 2005, 16, 1009-1019.
102.	Hilderbrand, A. E.; Clemmer, D. E. Determination of Sequence-Specific Intrinsic Size Parameters from Cross Sections for 162 Tripeptides, J. Phys. Chem B 2005, 109, 11802-11809.
101.	Julian, R. R.; Myung, S.; Clemmer, D. E. Do Homochiral Aggregates Have an Entropic Advantage? J. Phys. Chem. B 2005, 109, 440-444.
100.	Koeniger, S. L.; Valentine, S. J.; Myung, S.; Plasencia, M.; Lee, Y. L.; Clemmer, D. E. Development of Field Modulation in a Split-Field Drift Tube for High-Throughput Multi-dimensional Separations, J. Proteome Research 2005, 4, 25-35.
99.	Liu, X.; Plasencia, M.; Ragg, S.; Valentine, S. J.; Clemmer, D. E. Development of High-Throughput Dispersive LC-Ion Mobility-TOFMS Techniques for Analyzing the Human Plasma Proteome, Brief Funct Genomic Proteomic 2004, 3, 177-186.
98.	Nanita, S. C.; Takats, Z.; Myung, S.; Clemmer, D. E.; Cooks, R. G. Chiral Enrichment in Serine via Formation, Dissociation and Soft-Landing of Octameric Cluster Ions, J. Am. Soc. Mass Spectrom. 2004, 15, 1360-1365.
97.	Sowell, R. A.; Koeniger, S. L.; Valentine, S. J.; Moon, M. H.; Clemmer, D. E. Nanoflow LC/IMS-MS (and -CID/MS) of Protein Mixtures, J. Am. Soc. Mass Spectrom. 2004, 15, 1341-1353.
96.	Myung, S.; Julian, R. R.; Nantia, S. C.; Cooks, R. G.; Clemmer, D. E. Formation of Nanometer Scale Serine Clusters by Sonic Spray, J. Phys. Chem B 2004, 108, 6105-6111.
95.	Julian, R. R.; Myung, S.; Clemmer, D. E. Spontaneous Anti-Resolution in Heterochiral Clusters of Serine, J. Am. Chem. Soc. 2004, 126, 4110-4111.
94.	Counterman, A. E.; Clemmer, D. E. Anhydrous Polyproline Helices and Globules, J. Phys. Chem. B 2004, 108, 4885-4898.
93.	Srebalus Barnes, C. A.; Clemmer, D. E. Ion Mobility/Time-of-Flight Analysis of Combinatorial Library Mixtures in High Throughput Analysis: A Tool for Combinatorial Materials Science; Potyrailo, R. A. and Amis, E. J., Eds.; Kluwer Academic/Plenum Publishers: New York, NY, 2003, p. 187-216.
92.	Hilderbrand, A. E.; Myung, S.; Srebalus Barnes, C. A.; Clemmer, D. E. Development of LC-IMS-CID-TOFMS Techniques: Analysis of a 256 Component Tetrapeptide Combinatorial Library, J. Am. Soc. Mass Spectrom. 2003, 14, 1424-1436.
91.	Srebalus Barnes, C. A.; Clemmer, D. E. Assessing Intrinsic Side Chain Interactions Between i and i+4 Residues in Solvent-Free Peptides: A Combinatorial Gas-Phase Approach, J. Phys. Chem. A 2003, 107, 10566-10579. {invited for special issue honoring Charlie Parmenter}
90.	Moon, M. H.; Myung, S.; Plasencia, M.; Hilderbrand, A. E.; Clemmer, D. E. Nanoflow LC/Ion Mobility/CID/TOF for Proteomics: Analysis of a Human Urinary Proteome, J. Proteome Research 2003, 2, 589-597.
89.	Valentine, S. J.; Koeniger, S. L.; Clemmer, D. E. A Split-field Drift Tube for Separation and Efficient Fragmentation of Biomolecular Ions, Analytical Chemistry 2003, 75, 6202-6208.
88.	Myung, S.; Lee, Y. L.; Moon, M. H.; Taraszka, J. A.; Sowell, R.; Koeniger, S. L.; Hilderbrand A. E.; Valentine, S. J.; Cherbas, L.; Cherbas, P.; Kaufmann, T. C.; Miller, D. F.; Mechref, Y.; Novotny, M. V.; Ewing, M.; Clemmer D. E. Development of High-Sensitivity Ion Trap-IMS-TOF Techniques: A High-Throughput Nano-LC/IMS/TOF Separation of the Drosophila Fly Proteome, Analytical Chemistry 2003, 75, 5137-5145.
87.	Hilderbrand, A. E.; Valentine, S. J.; Clemmer, D. E. Mobilities: Biological Systems and Clusters in Encyclopedia of Mass Spectrometry (Theory and Ion Chemistry, Volume 1); Gross, M. L.; Caprioli, R. and Armentrout, P., Eds.; Elsevier: Kidlington, Oxford, 2003, p. 506-520.
86.	Que, A. H.; Mechref, Y.; Huang, Y.; Taraszka, J. A.; Clemmer, D. E.; Novotny, M. V. Coupling Capillary Electrochromatogarphy with Fourier-Transform Mass Spectrometry for Characterizing Complex Oligosaccharide Pools, Analytical Chemistry 2003, 75, 1684-1690.
85.	Counterman, A. E.; Clemmer, D. E. Compact -> Extended Helix Transitions of Polyalanine in Vacuo, J. Phys. Chem. B 2003, 107, 2111-2117.
84.	Counterman, A. E.; Thompson, M. S.; Clemmer, D. E. Identifying a protein by MALDI-TOF Mass Spectrometry: An Experiment for the Undergraduate Laboratory, J. of Chem. Edu. 2003, 80, 177-180.
83.	Lee, Y. J.; Hoaglund-Hyzer, C. S.; Srebalus Barnes, C. A.; Hilderbrand, A. E.; Valentine, S. J.; Clemmer, D. E. Development of High-Throughput LC-injected Ion Mobility-Q-TOF Techniques for Analysis of Complex Peptide Mixtures, J. Chromatography B 2002, 782, 343-351. {invited for the special Proteomics issue}
82.	Counterman, A. E.; Clemmer, D. E. Gas Phase Polyalanine: Assessment of i->i+3 and i->i+4 Helical Turns in [Ala_n+4H]⁴⁺ (n = 29 -49) Ion, J. Phys. Chem. B 2002, 106, 12045-12051.
81.	Myung, S.; Badman, E.; Lee, Y. J.; Clemmer, D. E. Structural Transitions of Electrosprayed Ubiquitin Ions Stored in an Ion Trap over ~10 ms to 30s, J. Phys. Chem. A 2002, 106, 9976-9982. {A special issue to celebrate Jack Beauchamp's 60^th birthday}
80.	Badman, E.; Myung, S.; Clemmer, D. E. Gas-Phase Separations of Protein and Peptide Ion Fragments Generated by Collision-Induced Dissociation in an Ion Trap, Analytical Chemistry 2002, 74, 4889-4894.
79.	Badman, E. R.; Hoaglund-Hyzer, C. S.; Clemmer, D. E. Dissociation of Different Conformations of Ubiquitin Ions, J. Am. Soc. Mass Spectrom. 2002, 13, 719-723.
78.	Valentine, S. J.; Clemmer, D. E. Temperature Dependent H/D Exchange of Compact and Elongated Cytochrome c Ions in the Gas Phase, J. Am. Soc. Mass Spectrom. 2002, 13, 506-517.
77.	Counterman, A. E.; Clemmer, D. E. Cis-Trans Signatures of Proline-Containing Tryptic Peptides in the Gas Phase, Analytical Chemistry 2002, 74, 1946-1951.
76.	Leavell, M. D.; Gaucher, S. P.; Leary, J. A.; Taraszka, J. A.; Clemmer, D. E. Conformational Studies of Zn-Ligand-Hexose Diastereomers Using Ion Mobility Measurements and Density Functional Theory Calculations, J. Am. Soc. Mass Spectrom. 2002, 13, 284-293.
75.	Mosier, P. D.; Counterman, A. E.; Jurs, P. C.; Clemmer, D. E. Prediction of Peptide Ion Collision Cross Sections from Topological Molecular Structure and Amino Acid Parameters, Analytical Chemistry 2002, 74, 1360-1370.
74.	Hoaglund-Hyzer, C. S.; Lee, Y. J.; Counterman, A. E.; Clemmer, D. E. Coupling Ion Mobility Separations, Collisional Activation Techniques, and Multiple Stages of MS for Analysis of Complex Peptide Mixtures, Analytical Chemistry 2002, 74, 992-1006.
73.	Kindy, J. M.; Taraszka, J. A.; Regnier, F. E.; Clemmer, D. E. Quantifying Peptides in Isotopically Labeled Protease Digests by Ion Mobility/Time-of-Flight Mass Spectrometry, Analytical Chemistry 2002, 74, 950-958.
72.	Srebalus Barnes, C. A.; Hilderbrand, A. E.; Valentine, S. J.; Clemmer, D. E. Resolving Isomeric Peptide Mixtures: A Combined HPLC/Ion Mobility-TOFMS Analysis of a 4000-Component Combinatorial Library, Analytical Chemistry 2002, 74, 26-36.
71.	Valentine, S. J.; Kulchania, M.; Srebalus Barnes, C. A.; Clemmer, D. E. Multidimensional separations of complex peptide mixtures: a combined high-performance liquid chromatography/ion mobility/time-of-flight mass spectrometry approach, Int. J. Mass Spectrom. 2001, 212, 97-109. {A special issue celebrating R. Graham Cooks' 60th birthday}
70.	Badman, E. R.; Hoaglund-Hyzer, C. S.; Clemmer, D. E. Monitoring Structural Changes of Proteins in an Ion Trap over ~10-200 ms: Unfolding Transitions in Cytochrome c Ions, Analytical Chemistry 2001, 73, 6000-6007.
69.	Counterman, A. E.; Clemmer, D. E. Magic Number Clusters of Serine in the Gas Phase, J. Phys. Chem. B 2001, 105, 8092-8096.
68.	Lee, Y. J.; Hoaglund-Hyzer, C. S.; Taraszka, J. A.; Zientara, G. A.; Counterman, A. E.; Clemmer, D. E. Collision-Induced Dissociation of Mobility-Separated Ions Using an Orifice-Skimmer Cone at the Back of a Drift Tube, Analytical Chemistry 2001, 73, 3549-3555.
67.	Counterman, A. E.; Hilderbrand, A. E.; Srebalus Barnes, C. A.; Clemmer, D. E. Formation of Peptide Aggregates during ESI: Size, Charge, Composition, and Contributions to Noise, J. Am. Soc. Mass Spectrom. 2001, 12, 1020-1035.
66.	Shvartsburg, A. A.; Siu, K. W. M.; Clemmer, D. E. Prediction of Peptide Ion Mobilities via a priori Calculations from Intrinsic Size Parameters of Amino Acid Residues, J. Am. Soc. Mass Spectrom. 2001, 12, 885-888.
65.	Johannessen, S. C.; Brisbois, R. G.; Fischer, J. P.; Grieco, P. A.; Counterman, A. E.; Clemmer, D. E. A Nano-Scale Barrel and Cube: Transition Metal-Mediated Self-Assembly of CpCoCb-Derived Ligand Scaffolds, J. Am. Chem. Soc. 2001, 123, 3818-3819.
64.	Ideue, S.; Sakamoto, K.; Honma, K.; Clemmer, D. E. Conformational change of electrosprayed cytochrome c studied by laser-induced fluorescence, Chem. Phys. Lett. 2001, 337, 79-84.
63.	Taraszka, J. A.; Counterman, A. E.; Clemmer, D. E. Gas-Phase separations of complex tryptic peptide mixtures, Fresenius J. Analytical Chemistry 2001, 369, 234-245.
62.	Counterman, A. E.; Clemmer, D. E. Large Anhydrous Polyalanine Ions: Evidence for Extended Helices and Onset of a More Compact State, J. Am. Chem. Soc. 2001, 123, 1490-1498.
61.	Taraszka, J. A.; Counterman, A. E.; Clemmer, D. E. Large anhydrous polyalanine ions: substitution of Na⁺ for H⁺ destabilizes folded states, Int. J. Mass Spectrom. 2001, 204, 87-100.
60.	Srebalus Barnes, C. A.; Clemmer, D. E. Assessment of Purity and Screening of Peptide Libraries by Nested Ion Mobility-TOFMS: Identification of RNase S-protein Binders, Analytical Chemistry 2001, 73, 424-433.
59.	Hoaglund-Hyzer, C. S.; Clemmer, D. E. Ion Trap/Ion Mobility/Quadrupole/Time-of-Flight Mass Spectrometry for Peptide Mixture Analysis, Analytical Chemistry 2001, 73, 177-184.
58.	Hoaglund-Hyzer, C. S.; Li, J.; Clemmer, D. E. Mobility Labeling for Parallel CID of Ion Mixtures, Analytical Chemistry 2000, 72, 2737-2740.
57.	Taraszka, J. A.; Li, J.; Clemmer, D. E. Metal-Mediated Peptide Ion Conformations in the Gas Phase, J. Phys. Chem. B 2000, 104, 4545-4551.
56.	Srebalus, C. A.; Li, J.; Marshall, W. S.; Clemmer, D. E. Determining Synthetic Failures in Combinatorial Libraries by Hybrid Gas-Phase Separation Methods, J. Am. Soc. Mass Spectrom. 2000, 11, 352-355.
55.	Valentine, S. J.; Counterman, A. E.; Clemmer, D. E. A Database of 660 Peptide Ion Cross Sections: Use of Intrinsic Size Parameters for Bona Fide Predictions of Cross Sections, J. Am. Soc. Mass Spectrom. 1999, 10, 1188-1211.
54.	Hoaglund Hyzer, C. S.; Counterman, A. E.; Clemmer, D. E. Anhydrous Protein Ions, Chem. Rev. 1999, 99, 3037-3079.
53.	Henderson, S. C.; Li, J.; Counterman, A. E.; Clemmer, D. E. Intrinsic Size Parameters for Val, Ile, Leu, Gln, Thr, Phe, and Trp Residues from Ion Mobility Measurements of Polyamino Acid Ions, J. Phys. Chem. B 1999, 103, 8780-8785.
52.	Srebalus, C. A.; Li, J.; Marshall, W. S.; Clemmer, D. E. Gas-Phase Separations of Electrosprayed Peptide Libraries, Analytical Chemistry 1999, 71, 3918-3927.
51.	Counterman, A. E.; Clemmer, D. E. Volumes of Individual Amino Acid Residues in Gas-Phase Peptide Ions, J. Am. Chem. Soc. 1999, 121, 4031-4039.
50.	Valentine, S. J.; Counterman, A. E.; Hoaglund-Hyzer, C. S.; Clemmer, D. E. Intrinsic Amino Acid Size Parameters from a Series of 113 Lysine-Terminated Tryptic Digest Peptide Ions, J. Phys. Chem. B 1999, 103, 1203-1207.
49.	Henderson, S. C.; Valentine, S. J.; Counterman, A. E.; Clemmer, D. E. ESI/Ion Trap/Ion Mobility/Time-of-Flight Mass Spectrometry for Rapid and Sensitive Analysis of Biomolecular Mixtures, Analytical Chemistry 1999, 71, 291-301.
48.	Valentine, S. J.; Counterman, A. E.; Hoaglund, C. S.; Reilly, J. P.; Clemmer, D. E. Gas-Phase Separations of Protease Digests, J. Am. Soc. Mass Spectrom. 1998, 9, 1213-1216.
47.	Li, J.; Taraszka, J. A.; Counterman, A. E.; Clemmer, D. E. Influence of solvent composition and capillary temperature on the conformations of electrosprayed ions: unfolding of compact ubiquitin conformers from pseudonative and denatured solutions, Int. J. Mass. Spectrom. 1999, 185/186/187, 37-47.
46.	Hoaglund, C. S.; Valentine, S. J.; Sporleder, C. R.; Reilly, J. P.; Clemmer, D. E. Three-Dimensional Ion Mobility/TOFMS Analysis of Electrosprayed Biomolecules, Analytical Chemistry 1998, 70, 2236-2242.
45.	Counterman, A. E.; Valentine, S. J.; Srebalus, C. A.; Henderson, S. C.; Hoaglund, C. S.; Clemmer, D. E. High-Order Structure and Dissociation of Gaseous Peptide Aggregates that are Hidden in Mass Spectra, J. Am. Soc. Mass Spectrom. 1998, 9, 743-759.
44.	Schroder, D.; Schwartz, H.; Clemmer, D. E.; Chen, Y.; Armentrout, P. B.; Baranov, V. I.; Bohme, D. K. Activation of Hydrogen and Methane by Thermalized FeO⁺ in the Gas Phase as Studied by Multiple Mass Spectrometric Techniques, Int. J. Mass Spectrom. Ion Proc. 1997, 161, 175-191.
43.	Hoaglund, C. S.; Valentine, S. J.; Clemmer, D. E. An Ion Trap Interface for ESI-Ion Mobility Experiments, Analytical Chemistry 1997, 69, 4156-4161.
42.	Liu, Y.; Valentine, S. J.; Counterman, A. E.; Hoaglund, C. S.; Clemmer, D. E. Injected-ion Mobility Analysis of Biomolecules, Analytical Chemistry 1997, 69, 728A.
41.	Hoaglund, C. S.; Liu, Y.; Ellington, A. D.; Pagel, M.; Clemmer, D. E. Gas-Phase DNA: Oligothymidine Ion Conformers, J. Am. Chem. Soc. 1997, 119, 9051-9052.
40.	Liu, Y.; Clemmer, D. E. Characterizing Oligosaccharides Using Injected-Ion Mobility/Mass Spectrometry, Analytical Chemistry 1997, 69, 2504-2509.
39.	Clemmer, D. E.; Jarrold, M. F. Ion Mobility Measurements and their Applications to Clusters and Biomolecules, J. Mass Spectrom. 1997, 32, 577-592.
38.	Valentine, S. J.; Counterman, A. E.; Clemmer, D. E. Conformer-Dependent Proton-Transfer Reactions of Ubiquitin Ions, J. Am. Soc. Mass Spectrom. 1997, 8, 954-961.
37.	Valentine, S. J.; Anderson, J. G.; Ellington, A. D.; Clemmer, D. E. Disulfide-Intact and -Reduced Lysozyme in the Gas Phase: Conformations and Pathways of Folding and Unfolding, J. Phys. Chem. B 1997, 101, 3891-3900.
36.	Valentine, S. J.; Clemmer, D. E. H/D Exchange Levels of Shape-Resolved Cytochrome c Conformers in the Gas Phase, J. Am. Chem. Soc. 1997, 119, 3558-3566.

35.	Dugourd, Ph.; Hudgins, R. R.; Clemmer, D. E.; Jarrold, M. F. High-resolution ion mobility measurements, Rev. Sci. Instrum. 1997, 68, 1122-1129.
34.	Shelimov, K. B.; Clemmer, D. E.; Hudgins, R. R.; Jarrold, M. F. Protein Structure in Vacuo: The Gas Phase Conformations of BPTI and Cytochrome c, J. Am. Chem. Soc. 1997, 119, 2240-2248.
33.	Shelimov, K. B.; Clemmer, D. E.; Jarrold, M. F. Metal Containing Carbon Clusters, J. Chem. Soc. Dalton Trans. 1996, 567-574.
32.	Shelimov, K. B.; Clemmer, D. E.; Hunter, J. M.; Jarrold, M. F. Ion Mobility Studies of the Structures and Isomerization of Gas Phase Carbon and Metal Containing Carbon Clusters, in The Chemical Physics of Fullerenes 10 (and 5) Years Later; NATO-ASI Series E, (Kluwer, Dordrecht, 1996) p. 71-87.
31.	Clemmer, D. E.; Hudgins, R. R.; Jarrold, M. F. Naked Protein Conformations: Cytochrome c in the Gas Phase, J. Am. Chem. Soc. 1995, 117, 10141-10142.
30.	Shelimov, K. B.; Clemmer, D. E.; Jarrold, M. F. Drift Tube Studies of Metallofullerenes, in Recent Advances in the Chemistry and Physics of Fullerenes and Related Materials (Proceedings of The Electrochemical Society Vol. 95-10), R. S. Ruoff and K. M. Kadish, Eds., (The Electrochemical Society, Pennington, NJ, 1995) p. 1437-1447.
29.	Shelimov, K. B.; Clemmer, D. E.; Jarrold, M. F. Structures and Isomerization of LaC_n⁺ Clusters, J. Phys. Chem. 1995, 99, 11376-11386.
28.	Clemmer, D. E.; Jarrold, M. F. Metal-Containing Carbon Clusters: Structures, Isomerization, and Formation of NbC_n⁺ Clusters, J. Am. Chem. Soc. 1995, 117, 8841-8850.
27.	Clemmer, D. E.; Hunter, J. M.; Shelimov, K. B.; Jarrold, M. F. Physical and Chemical Evidence for Metallofullerenes with Metal Atoms as Part of the Cage, Nature 1994, 372, 248-250.
26.	Chen, Y.M.; Clemmer, D. E.; Armentrout, P. B. Kinetic and Electronic Energy Dependence of the Reactions of Sc⁺ and Ti⁺ with D₂O, J. Phys. Chem. 1994, 98, 11490-11498.
25.	Shelimov, K. B.; Clemmer, D. E.; Jarrold, M. F. Structures and Formation of Small LaC_n⁺ Metallofullerenes, J. Phys. Chem. 1994, 98, 12819-12821.
24.	Honma, K.; Nakamura, M.; Clemmer, D. E.; Koyano, I. Kinetics of Ti (a³F, a⁵F) and V(a⁴F, a⁶D) Depletion by NH₃ and H₂S, J. Phys. Chem. 1994, 98, 13286-13293.
23.	Honma, K.; Clemmer, D. E. The Importance of the Electron Transfer Mechanism in Reactions of Neutral Transition Metal Atoms, Laser Chem. 1994, 15, 209-220.
22.	Chen, Y. M.; Clemmer, D. E.; Armentrout, P. B. Conversion of CH₄ to CH₃OH: Reactions of CoO⁺ with CH₄ and D₂, Co⁺ with CH₃OD and D₂O, and Co⁺(CH₃OD) with Xe, J. Am. Chem. Soc. 1994, 116, 7815-7826.
21.	Clemmer, D. E.; Shelimov, K. B.; Jarrold, M. F. Bonding of Metals to Carbon Rings: LaC_n⁺ Isomers with La⁺ Inserted and Attached to the Ring, J. Am. Chem. Soc. 1994, 116, 5971-5972.
20.	Clemmer, D. E.; Chen, Y. M.; Khan, F. A.; Armentrout, P. B. State-Specific Reactions of Fe⁺(a⁶D, a⁴F) with D₂O and Reactions of FeO⁺ with D₂, J. Phys. Chem. 1994, 98, 6522-6529.
19.	Clemmer, D. E.; Chen, Y. M.; Aristov, N.; Armentrout, P. B. Kinetic and Electronic Energy Dependence of the Reaction V+ with D₂O, J. Phys. Chem. 1994, 98, 7538-7544.
18.	Clemmer, D. E.; Jarrold, M. F. Structural Dynamics of Carbon and Metal Containing Carbon Clusters, in Laser Techniques for State-Selected and State-to-State Chemistry II, SPIE Proc. 1994, 2124, 400.
17.	Clemmer, D. E.; Shelimov, K. B.; Jarrold, M. F. Gas-Phase Self-Assembly of Endohedral Metallofullerenes, Nature 1994, 367, 718-720.
16.	Clemmer, D. E.; Honma, K.; Koyano, I. Kinetics of Excited State Ti(a⁵F) Depletion by NO, O₂, N₂O, and N₂, J. Phys. Chem. 1993, 97, 11480-11488.
15.	Khan, F. A.; Clemmer, D. E.; Schultz, R. H.; Armentrout, P. B. Sequential Bond Energies of Cr(CO)_x⁺, x = 1 - 6, J. Phys. Chem. 1993, 97, 7978-7987.
14.	Chen, Y. M.; Clemmer, D. E.; Armentrout, P. B. Gas-phase thermochemistry of VH and CrH, J. Chem. Phys. 1993, 98, 4929-4936.
13.	Clemmer, D. E.; Aristov, N.; Armentrout, P. B. Reactions of ScO⁺, TiO⁺, and VO⁺ with D₂: M⁺-OH Bond Energies and Effects of Spin Conservation, J. Phys. Chem. 1993, 97, 544-552.
12.	Clemmer, D. E.; Weber, M. E.; Armentrout, P. B. Reactions of Al⁺(¹S) with NO₂, N₂O and CO₂: Thermochemistry of AlO and AlO⁺, J. Phys. Chem. 1992, 96, 10888-10893.
11.	Clemmer, D. E.; Armentrout, P. B. Direct determination of the adiabatic ionization energy of NO₂ as measured by guided ion-beam mass spectrometry, J. Chem. Phys. 1992, 97, 2451-2458.
10.	Armentrout, P. B.; Clemmer, D. E. Guided Ion Beam Studies of the Energetics of Organometallic Species, in Energetics of Organometallic Species, Simoes, J. A. M., Eds.; Kluwer: Netherlands, 1992; pp. 321-356.
9.	Clemmer, D. E.; Dalleska, N. F.; Armentrout, P. B. Gas-Phase Thermochemistry of the Group 3 Dioxides: ScO₂, YO₂ and LaO₂, Chem. Phys. Lett. 1992, 190, 259-265.
8.	Clemmer, D. E.; Dalleska, N. F.; Armentrout, P. B. Reaction of Zn⁺ with NO₂. The gas-phase thermochemistry of ZnO, J. Chem. Phys. 1991, 95, 7263-7268.
7.	Clemmer, D. E.; Elkind, J. L.; Aristov, N.; Armentrout, P. B. Reaction of Sc⁺, Ti⁺, and V⁺ with CO. MC⁺ and MO⁺ bond energies, J. Chem. Phys. 1991, 95, 3387-3393.
6.	Chen, Y.M.; Clemmer, D. E.; Armentrout, P. B. The gas-phase thermochemistry of TiH, J. Chem. Phys. 1991, 95, 1228-1233.
5.	Clemmer, D. E.; Armentrout, P. B. Ammonia Activation by Co⁺, Ni⁺, and Cu⁺. M⁺-NH₂ Bond Energies and M⁺NH₃ Adduct Lifetimes, J. Phys. Chem. 1991, 95, 3084-3090.
4.	Fisher, E. R.; Elkind, J. L.; Clemmer, D. E.; Georgiadis, R.; Loh, S. K.; Aristov, N.; Sunderlin, L. S.; Armentrout, P. B. Reactions of fourth-period metal ions (Ca⁺ - Zn⁺) with O₂: Metal-oxide ion bond energies, J. Chem. Phys. 1990, 93, 2676-2691.
3.	Clemmer, D. E.; Sunderlin, L. S.; Armentrout, P. B. Ammonia Activation by Sc⁺ and Ti⁺: Electronic and Translational Energy Dependence, J. Phys. Chem. 1990, 94, 3008-3015.
2.	Clemmer, D. E.; Sunderlin, L. S.; Armentrout, P. B. Ammonia Activation by V⁺: Electronic and Translational Energy Dependence, J. Phys. Chem. 1990, 94, 208-217.
1.	Clemmer, D. E.; Armentrout, P. B. Investigation of Isomeric Intermediates: Co⁺-NH₃ and H-Co⁺-NH₂, J. Am. Chem. Soc. 1989, 111, 8280-8281.

Last modified: July 14, 2008