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Clemmer Group

List of Publications


Links to PDF versions of publications are provided where possible and may be viewed with Adobe Acrobat Reader. Additionally, permalinks (and outside links for book chapters) are provided for publisher information. Important papers are highlighted in IU Leather. This list current as of 11 December 2023.




    Published:


    2022

  1. PATENT Jarrold, M. F.; Clemmer, D.E.; Draper, B. E.; Barnes, L.F. System and Method for Processing Virus Preparations to Reduce Heterogeneity. US Patent Office. 2023. US20230048598A1
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  2. PATENT Jarrold, M. F.; Clemmer D. E. Charge Filter Arrangment and Applications Thereof. US Patent Office. 2023. US20230039701A1
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  3. PATENT Jarrold, M. F.; Clemmer D. E. Mass Spectrometer with Charge Measurement Arrangement. US Patent Office. 2023. US20230013173A1
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  4. Becket, D.; El-Baba, T. J.; Zhang, Z.; Clemmer, D. E.; Raghavachari, K. Tautomerization of H+KPGG: Entropic Consequences of Strong Hydrogen-Bond Networks in Peptides J. Phys. Chem. A 2023 XXXX, XXX, XXXX–XXXX. doi.org/10.1021/acs.jpca.3c03744
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  5. Anthony, A. J.; Gautam, A. K. S.; Miller, L. M.; Ma, Y.; Hardwick, A. G.; Sharma, A.; Ghatak, S.; Matouschek, A.; Jarrold, M. F.; and Clemmer, D. E. CDMS Analysis of Intact 19S, 20S, 26S, and 30S Proteasomes: Evidence for Higher-Order 20S Assemblies at a Low pH Anal. Chem. 2023 95, 33, 12209–12215. doi.org/10.1021/acs.analchem.3c00472
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  6. Sharon, E. M.; Henderson,; Clemmer, D. E. Resolving Hidden Solution Conformations of Hemoglobin Using IMS-IMS on a Cyclic Instrument J. Am. Soc. Mass Spectrom 2023 34, 8, 1559–1568. doi.org/10.1021/jasms.3c00032
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  7. Henderson, L. W.; Sharon, E. M.; Amit, K.S.; Anthony, A. J.; Jarrold, M. F.; Russell, D. H.; Matouschek, A.; Clemmer, D. E. Stability of 20S Proteasome Configurations: Preopening the Axial Gate J. Phys. Chem. Letters 2023 14, 21, 5014–5017. doi.org/10.1021/acs.jpclett.3c01040
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  8. Sarbu, M.; Ica, R.; Sharon, E. M.; Clemmer, D. E.; Zamfir, A. D. Glycomics by Ion Mobility Tandem Mass Spectrometry of Chondroitin Sulfate Disaccharide Domain in Biglycan Anal. Sci. 2023 58, 3, 4908. doi.org/10.1002/jms.4908
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    Published:


    2022

  9. PATENT Clemmer, D. E.; El-Baba, T. J.; Fuller, D. R.; Woodall, D. W.; Russell, D. H.; Williams, E. R. Instrument and method for energizing molecules in charged droplets. US Patent Office. 2022. US11420205B2
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  10. PATENT Clemmer, D. E.; Jarrold, M. F.; El-Baba, T. J.; Lutomski, C. A. Identification of sample subspecies based on particle mass and charge over a range of sample temperatures. US Patent Office. 2022. US20220216047A1
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  11. Sarbu, M.; Fabris, D.; Vukelic, Z.; Clemmer, D. E.; Zamfir, A. D. Ion Mobility Mass Spectrometry Reveals Rare Sialylated Glycosphingolipid Structures in Human Cerebrospinal Fluid Molecules 2022 27, 3, 743. doi.org/10.3390/molecules27030743
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  12. Walker, T. E.; Shirzadeh, M.; He Mirabel Sun; McCabe, J. W.; Roth, A.; Moghadamchargari, Z.; Clemmer, D. E.; Laganowsky, A.; Rye, H.; Russell, D. H. Temperature Regulates Stability, Ligand Binding (Mg2+ and ATP), and Stoichiometry of GroEL–GroES Complexes J. Am. Chem. Soc. 2022 144, 6, 2667–2678. doi.org/10.1021/jacs.1c11341
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  13. Laganowsky, A.; Clemmer, D. E.; Russell, D. H. Variable-Temperature Native Mass Spectrometry for Studies of Protein Folding, Stabilities, Assembly, and Molecular Interactions Annual Reviews 2022 51, 63–77. doi.org/10.1146/annurev-biophys-102221-101121
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  14. Sarbu, M.; Ica, R.; Sharon, E.; Clemmer, D. E.; Zamfir, A. D. Identification and Structural Characterization of Novel Chondroitin/Dermatan Sulfate Hexassacharide Domains in Human Decorin by Ion Mobility Tandem Mass Spectrometry Molecules 2022 27, 18, 6026. doi.org/10.3390/molecules27186026
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  15. Zeng, X.; Novotny, M. V.; Clemmer, D. E.; Trinidad, J. C. A graphical representation of glycan heterogeneity Glycobiology 2022 32, 3, 201–207. doi.org/10.1093/glycob/cwab116
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  16. Zhang, Z.; Conant, C. R.; El-Baba, T. J.; Raab, S. A.; Fuller, D. R.; Hales, D. A.; Clemmer, D. E. Diketopiperazine Formation from FPGnK (n = 1–9) Peptides: Rates of Structural Rearrangements and Mechanisms J. Phys. Chem. B. 2022 125, 29, 8107–8116. doi.org/10.1021/acs.jpcb.1c03515
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  17. Zhang, Z.; Hales, D. A.; Clemmer, D. E. Influence of N Terminus Amino Acid on Peptide Cleavage in Solution through Diketopiperazine Formation J. Am. Soc. Mass. Spectrom. 2022 33, 88, 1368–1376. doi.org/10.1021/jasms.2c00037
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  18. Brown, B. A.; Guda, P. R.; Zeng, X.; Anthony, A. J.; Couse, A. D.; Barnes, L.F.; Sharon, E. M.; Trinidad, J. C.; Sen, C. K.; Jarrold, M. F.; Ghatak, S.; Clemmer, D. E. Analysis of Keratinocytic Exosomes from Diabetic and Nondiabetic Mice by Charge Detection Mass Spectrometry Anal. Chem. 2022 94, 25, 8909–8918. doi.org/10.1021/acs.analchem.2c00453
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    2021

  19. PATENT Clemmer, D. E.; Koeniger, S. L.; Valentine, J. S. Ion Mobility Spectrometer. EU Patent Specification. 2022. EP1952421B1
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  20. Sarbu, M. D.; Vukelic, Z.; Clemmer, D. E.; Zamfir, A. D. Ion mobility mass spectrometry reveals novel and rare ganglioside structures in human cerebrospinal fluid. Febs. Open. Bio 2021 11, 212–212.
  21. Zamfir, A. D.; Sarbu, M.; Ica, R.; Clemmer, D. E.; Vkelic, Z. Brain glycomics by novel mass spectrometry approaches based on ion mobility and chipnanoelectrospray ionization. Febs. Open. Bio 2021 11, 67–67.
  22. Qiao, P.; Schrecke, S.; Walker, T.; McCabe, J. W.; Lyu, J.; Zhu, Y.; Zhang, T.; Kumar, S.; Clemmer, D. E.; Russell, D. H.; Laganowsky, A. Entropy in the Molecular Recognition of Membrane Protein–Lipid Interactions J. Phys. Chem. Lett. 2021 12, 51, 12218–12224. doi.org/10.1021/acs.jpclett.1c03750
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  23. Raab, S. A.; El-Baba, T. J.; Laganowsky, A.; Russell, D. H.; Valentine, S. J.; Clemmer, D. E. Protons Are Fast and Smart; Proteins Are Slow and Dumb: On the Relationship of Electrospray Ionization Charge States and Conformations J. Am. Soc. Mass. Spectrom. 2021 32,7 1553–1561. doi.org/10.1021/jasms.1c00100
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  24. El-Baba, T. J.; Raab, S. A.; Buckley, R. P.; Brown, C. J.; Lutomski, C. A.; Henderson, L. W.; Woodall, D. W.; Shen, J.; Trinidad, J. C.; Niu, H.; Jarrold, M. F.; Russell, D. H.; Laganowsky, A.; Clemmer, D. E. Thermal Analysis of a Mixture of Ribosomal Proteins by vT-ESI-MS: Toward a Parallel Approach for Characterizing the Stabilitome. Anal. Chem. 2021, 93, 8484–8492. doi.org/10.1021/acs.analchem.1c00772
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  25. Russell, D. H.; Clemmer, D. E. Focus on Ionization Technologies Used in MS: Fundamentals and Applications, Honoring Dr. Sarah Trimpin, Recipient of the 2019 ASMS Biemann Medal. J. Am. Soc. Mass Spectrom. 2021, 32, 3, 616–617. doi.org/10.1021/jasms.1c00030
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  26. Zhang, Z.; Raab, S. A.; Hales, D. H.; Clemmer, D. E. Influence of solvents upon diketopiperazine (DKP) formation of FPG8K. J. Phys. Chem. B 2021, 125, 11, 2952–2959. doi.org/10.1021/acs.jpcb.1c00269
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  27. Miller, L. M.; Barnes, L. F.; Raab, S. A.; Draper, B. E.; El-Baba, T. J.; Lutomski, C. A.; Robinson, C. V.; Clemmer, D. E.; and Jarrold, M. F. Heterogeneity of Glycan Processing on Trimeric SARS-CoV-2 Spike Protein Revealed by Charge Detection Mass Spectrometry. J. Am. Chem. Soc. 2021, 143, 10, 3959–3966. doi.org/10.1021/jacs.1c00353
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  28. McCabe, J. W.; Shirzaden, M.; Walker, T. E.; Lin, C., Jones, B. J.; Wysocki, V. H.; Barondeau, D. P.; Clemmer, D. E.; Laganowsky, A.; Russell, D. E. Variable-Temperature Electrospray Ionization for Temperature-Dependent Folding/Refolding Reactions of Proteins and Ligand Binding. Anal. Chem.. 2021, 93, 18, 6924–6931. doi.org/10.1021/acs.analchem.1c00870
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  29. Sarbu, M.; Petrica, L.; Clemmer, D. E.; Vukelic, Z.; Zamfir, A. D. Gangliosides of Human Glioblastoma Multiforme: A Comprehensive Mapping and Structural Analysis by Ion Mobility Tandem Mass Spectrometry. J. Am. Soc. Mass Spectrom.. 2021, 32, 5, 1249–1257. doi.org/10.1021/jasms.1c00088
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  30. Bera, S.; Dong, X.; Krishnarjuna, B.; Raab, S. A.; Hales, D. A.; Ji, W.; Tang, Y.; Shimon, L. J. W.; Ramamoorthy, A.; Clemmer, D. E.; Wei, G.; Gazit, E. Solid-state packing dictates the unexpected solubility of aromatic peptides Cell Rep. Phys. Sci. 2021, 2, 4, 100391. doi.org/10.1016/j.xcrp.2021.100391
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  31. Inutan, E. D.; Jarois, D. R.; Lietz, C. B.; El-Baba, T. J.; Elia, E. A.; Karki, S.; Sampat, A. A. S.; Foley, C. D.; Clemmer, D. E.; Trimpin, S. Comparison of gaseous ubiquitin ion structures obtained from a solid and solution matrix using ion mobility spectrometry/mass spectrometry Rap. Com. Mass Spectrom.. 2021, 35, 1, 8793. doi.org/10.1002/rcm.8793
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    2020

  32. PATENT Rizzo. T.; Masellis, C.; Kamarath, M. Z.; Clemmer, D. E.; Khanal, N. Method for characterizing polysaccharides. US Pattent Office. 2020. US10845337B2
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  33. PATENT Clemmer, D. E.; Ewing, M. A. Closed path ion mobility spectrometer having a common ion inlet and outlet . US Pattent Office. 2020. US10788453B2
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  34. Moghadamchargari Z,; Huddleston J,; Shirzadeh M,; Zheng X,; Clemmer D.E.,; Russell D.H.,; Laganowsky A. Intrinsic GTPase Activity of K-RAS Monitored by Native Mass Spectrometry. Biochemistry 2020, 58, 31,, 3396–3405,doi.org/10.1021/acs.biochem.9b00532
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  35. Zhou X.; Brown B.A.; Siegel A.P.; El Masry M.S.; Zeng X.; Song W.; Das A.; Khandelwal P.; Clark A.; Singh K.; Guda P.R. Exosome-Mediated Crosstalk between Keratinocytes and Macrophages in Cutaneous Wound Healing. ACS nano. 2020, 14,10, 12732–12748,doi.org/10.1021/acsnano.0c03064
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  36. Brown C.J.; Gaunitz S.; Wang Z.; Strindelius L.; Jacobson S.C.; Clemmer D.E.; Trinidad J.C.; Novotny M.V. Glycoproteomic Analysis of Human Urinary Exosomes. Anal. Chem. 2020, 92, 14357–14365, doi.org/10.1021/acs.analchem.0c01952
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  37. Sarbu, M.; Clemmer, D. E.; Zamfir, A. D. Ion mobility mass spectrometry of Human Melanoma Gangliosides. J. Biochi. 2020, 177, 226–237, doi.org/10.1016/j.biochi.2020.08.011
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  38. Raab, S. A.; El-Baba, T. J.; Woodall, D. W.; Liu, W.; Liu, Y.; Baird, Z.; Hales, D. A.; Laganowsky, A.; Russell, D. H.; Clemmer, D. E. Evidence for Many Unique Solution Structures for Chymotrypsin Inhibitor 2: A Thermodynamic Perspective Derived from vT-ESI-IMS-MS Measurements. J. Amer. Chem. Soc. 2020, 142,41, 17372–17383, DOI: 10.1021/jacs.0c05365
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  39. Woodall, D. W.; Henderson, L. W.; Raab, S. A.; Honma, K.; Clemmer, D. E. Understanding the Thermal Denaturation of Myoglobin with IMS-MS: Evidence for Multiple Stable Structures and Trapped Pre-equilibrium States, J. Amer. Soc. Mass Spectrom. 2020, 32,1, 64–72, doi.org/10.1021/jasms.0c00075
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  40. Austin, C.A.; Inutan, E.D.; Bohrer, B.C.; Li, J.; Fischer, J.L.; Wijerathane, K.; Foley, C.D.; Lietz, C.B.; Woodall, D.W.; Imperial, L.F.; Clemmer, D.E. Resolving Isomers of Star-Branched Poly (Ethylene Glycols) by IMS-MS using Multiply-Charged Ions. J. Amer. Soc. Mass Spectrom. 2020, 32,1, 21–32, doi.org/10.1021/jasms.0c00045
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  41. Sarbu, M.; Raab, S. A.; Henderson, L.W.; Fabris, D.; Vukelić, Ž.; Clemmer, D. E.; Zamfirad, A. D. Cerebrospinal fluid: Profiling and fragmentation of gangliosides by ion mobility mass spectrometry. Biochimie. 2020, 170, 36–48,doi.org/10.1016/j.biochi.2019.12.008
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  42. Woodall, D. W.; Brown, C. J.; Raab, S. A.; El-Baba, T. J.; Laganowsky, A.; Russel, D. H.; Clemmer, D. E. Melting of Hemoglobin in Native Solutions as measured by IMS-MS, Anal. Chem. 2020, 92,4, 3440–3446, doi.org/10.1021/acs.analchem.9b05561
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  43. Brown, B. A.; Xuyao, Z. ; Todd, A. R.; Barnes, L. F.; Winstone, J. M. A.; Trinidad, J. C.; Novotny, M. V.; Jarrold, M. F.; Clemmer, D. E. Charge Detection Mass Spectrometry Measurements of Exosomes and other Extracellular Particles Enriched from Bovine Milk, Anal. Chem. , 2020, 92, 4, 3285–3292,doi.org/10.1021/acs.analchem.9b05173
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    2019

  44. PATENT Ewing, M. A.; Clemmer, D. E.; Hybrid ion mobility spectrometer. US Pattent Office. 2019. US10234423B2
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  45. Woodall, D. W.; El-Baba, T. J.; Fuller, D. R.; Liu, W..; Brown, C. J.; Laganowsky, A.; Russel, D. H.; Clemmer, D. E. Variable-Temperature ESI-IMS-MS Analysis of Myohemerythrin Reveals Ligand Losses, Unfolding, and a Non-Native Disulfide Bond, Anal. Chem. , 2019, 91, 10, 6808–6814, doi.org/10.1021/acs.analchem.9b00981
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  46. Brown, C. J.; Grassmyer, K. T.; MacDonald, M.; Clemmer, D. E.; Trinidad, J. C. Glycoproteome Analysis of Human Serum and Brain Tissue, bioRxiv , 2019, doi.org/10.1101/647081
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  47. Brown, C. J.; Woodall, D. W.; El-Baba, T. J.; Clemmer, D. E. Characterizing Thermal Transitions of IgG with Mass Spectrometry, J. Am. Soc. Mass Spectrom., DOI: doi.org/10.1007/s13361-019-02292-6
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  48. Beckett, D.; El-Baba, T. J.; Gilbert, K.; Clemmer, D. E.; Raghavachari, K. Untangling Hydrogen Bond Networks with Ion Mobility Spectrometry and Quantum Chemical Calculations: A Case Study on H+XPGG, J. Phys. Chem. B., 2019, 123(27), 5370–5741, doi.org/10.1021/acs.jpcb.9b03803
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  49. El-Baba, T. J.; Clemmer, D. E. Solution thermochemistry of concanavalin A tetramer conformers measured by variable-temperature ESI-IMS-MS, Int. J. Mass Spectrom., 2019, 443, 93–100, DOI: doi.org/10.1016/j.ijms.2019.06.004.
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  50. Chen, X.; Raab, S.; Poe, T.; Clemmer, D. E.; Larriba-Andaluz, C. Determination of Gas-Phase Ion Structures of Locally Polar Homopolymers Through High-Resolution Ion Mobility Spectrometry–Mass Spectrometry, J. Am. Soc. Mass Spectrom., 2019, 30, 905–918, DOI: 10.1007/s13361-019-02184-9
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  51. Dunbar, C. A.; Rayaprolu, V.; Wang, J. C.-Y.; Brown, C. J.; Leishman, E.; Jones-Burrage, S.; Trinidad, J. C.; Bradshaw, H. B.; Clemmer, D. E.; Mukhopadhyay, S.; Jarrold, M. F. Dissecting the Components of Sindbis Virus from Arthropod and Vertebrate Hosts: Implications for Infectivity Differences, ACS Infect Dis., 2019, 5, 6, 892–902, DOI: 10.1021/acsinfecdis.8b00356
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  52. Conant, C. R.; Fuller, D. R.; Zhang, Z.; Woodall, D. W.; Russell, D. H.; Clemmer, D. E. Substance P in the Gas Phase: Conformational Changes and Dissociations Induced by Collisional Activation in a Drift Tube , J. Am. Soc. Mass Spectrom., 2019, 30, 932–945, DOI: 10.1007/s13361-019-02160-3
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  53. Conant; C. R.; Fuller, D. R.; El-Baba, T. J.; Zhang, Z.; Russell, D. H.; Clemmer, D. E. Substance P in Solution: Trans-to-Cis Configurational Changes of Penultimate Prolines Initiate Non-enzymatic Peptide Bond Cleavages, J. Am. Soc. Mass Spectrom., 2019, 30, 919–931, DOI: 10.1039/C9SC00704K
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  54. Sahota, N.; AbuSalim, D. I.; Wang, M. L.; Brown, C. J.; Zhang, Z.; El-Baba, T. J.; Cook, S. P.; Clemmer, D. E. A microdroplet-accelerated Biginelli reaction: mechanisms and separation of isomers using IMS-MS, Chem. Sci., 2019, 10, 4822–4827, DOI: 10.1039/C9SC00704K
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  55. Fuller, D. R.; Conant, C. R.; El-Baba, T. J.; Zhang, Z.; Molloy, K. R.; Zhang, C. S.; Hales, D. A.; Russell, D. H.; Clemmer, D. E. Monitoring the stabilities of a mixture of peptides by mass-spectrometry-based techniques, EJMS., 2019, 25, 73–81
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  56. El-Baba, T. J.; Fuller, D. R.; Hales, D. A.; Russell, D. H.; Clemmer, D. E. Solvent Mediation of Peptide Conformations: Polyproline Structures in Water, Methanol, Ethanol, and 1-Propanol as Determined by Ion Mobility Spectrometry-Mass Spectrometry, J. Am. Soc. Mass Spectrom., 2019, 30, 77–84, DOI: 10.1007/s13361-018-2034-7
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    2018

  57. PATENT Clemmer, D. E.; Ewing, M. A. Ion mobility spectrometer and method of operating same. US Pattent Office. 2018. US20190017963A1
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  58. Musbat, L.; Assis, S.; Dilger, J. M.; El-Baba, T. J.; Fuller, D. R.; Knudsen, J. L.; Kiefer, H. V.; Hirshfeld, A.; Friedman, N.; Andersen, L. H.; Sheves, M.; Clemmer, D. E.; Toker, Y. Action and Ion Mobility Spectroscopy of a Shortened Retinal Derivative, J. Am. Soc. Mass Spectrom., 2018, 29, 2152–2159, DOI: 10.1007/s13361-018-2033-8
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  59. Beckett, D.; El-Baba, T. J.; Clemmer, D. E.; Raghavachari, K. Electronic Energies Are Not Enough: An Ion Mobility-Aided, Quantum Chemical Benchmark Analysis of H+GPGG Conformers, J. Chem. Theory Comput., 2018, 14, 5406–5418, DOI: 10.1021/acs.jctc.8b00648
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  60. Fuller, D. R.; Conant, C. R.; El-Baba, T. J.; Brown, C. J.; Woodall, D. W.; Russell, D. H.; Clemmer, D. E. Conformationally regulated peptide bond cleavage in bradykinin, J. Am. Chem. Soc., 2018, 140, 9357–9360, DOI: 10.1021/jacs.8b04751
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  61. Lavine, B. K.; White, C. G.; Ding, T.; Gaye, M. M.; Clemmer, D. E. Wavelet based classification of MALDI-IMS-MS spectra of serum N-Linked glycans from normal controls and patients diagnosed with Barrett's esophagus, high grade dysplasia, and esophageal adenocarcinoma, Chemometrics and Intelligent Laboratory Systems, 2018, 176, 74–81, DOI: 10.1016/j.chemolab.2018.03.008
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  62. Khanal, N.; Gaye, M. M.; Clemmer, D. E. Multiple Solution Structures of the Disordered Peptide Indolicidin from IMS-MS Analysis, Int. J. Mass Spectrom. , 2018, 427, 52–58, DOI: 10.1016/j.ijms.2017.09.009
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  63. Brown, C. J.; Kaufman, T.; Trinidad, J. C.; Clemmer, D. E. Proteome changes in the aging Drosophila melanogaster, Int. J. Mass Spectrom., 2018, 425, 36–46, DOI: 10.1093/nar/gkx1087
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  64. Sarbu, M; Vukelic, Z; Clemmer, D. E.; Zamfir, A. D. Ion mobility mass spectrometry provides novel insights into the expression and structure of gangliosides in normal adult human hippocampus , Analyst, 2018, 143, 5234–5246, DOI: 10.1039/C8AN01118D
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  65. El-Baba, T. J.; Fuller, D. R.; Woodall, D. W.; Raab, S. A.; Conant, C. R.; Dilger, J. M.; Toker, Y.; Williams, E. R.; Russell, D. H.; Clemmer, D. E. Melting Proteins Confined in Nanodroplets with 10.6 μm Light Provides Clues about Early Steps of Denaturation, Chem. Commun., 2018, 54, 3270–3273, DOI: 10.1039/C7CC09829D
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  66. Khanal, N.; Masellis, C.; Kamrath, M. Z.; Clemmer, D. E.; Rizzo, T. R. Cryogenic IR spectroscopy Combined with Ion Mobility Spectrometry for the Analysis of Human Milk Oligosaccharides, Analyst, 2018, 143, 1846–1852, DOI: 10.1039/C8AN00230D
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  67. Jacobs, A. D.; Jovan Jose, K. V.; Horness, R.; Raghavachari, K.; Thielges, M. C.; Clemmer, D. E. Cooperative Formation of Icosahedral Proline Clusters from Dimers, J. Am. Soc. Mass Spectrom., 2018, 29, 95–102, DOI: 10.1007/s13361-017-1833-6
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  68. Glauninger, H.; Zhang, Y.; Higgins, K. A.; Jacobs, A. D.; Martin, J. E.; Fu, Y.; Coyne, H. J.; Bruce, K. E.; Maroney, M. J.; Clemmer, D. E.; Capdevila, D. A.; Giedroc, D. P. Metal-dependent allosteric activation and inhibition on the same molecular scaffold: the copper sensor CopY from Streptococcus pneumoniae Chem. Sci., 2018, 9, 105–118, DOI: 10.1039/C7SC04396A
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  69. Gilmore, C.; Dsch, M.; Sward, E.; Hales, D.; Fuller, D.; El-Baba, T.; Clemmer D. E. Activation parameters for peptide cleavage at the penultimate residue: Dependence on identity of Yyy in XxxYyyGlyGly. Abstracts of Papers Am. Chem. Soc. 2018
  70. Dsch, M.; Sward, E.; Gilmore, C.; Hales, D.; Fuller, D.; El-Baba, T.; Clemmer D. E. Measurement of the activation parameters for fragmentation at penultimate proline in three tetrapeptides. Abstracts of Papers Am. Chem. Soc. 2018

    71. 2017

  71. PATENT Clemmer, D. E.; Ewing, M. A. Ion mobility spectrometer and method of operating same. US Pattent Office. 2017. US10024821B2
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  72. Glass, A. T.; Dickerson, K.; Hales, D. E.; El-Baba, T. J.; Clemmer, D. E. Survey of proline conformational behavior in protonated gas-phase XxxProGlyGly. Abs. Papers Amer. Chem. Soc. , 2017
  73. Dickerson, K.; Glass, A. T.; Hales, D. E.; El-Baba, T. J.; Clemmer, D. E. Gas-phase measurement of the barrier to cis-trans interconversion of proline in a tetrapeptide. Abs. Papers Amer. Chem. Soc. , 2017
  74. Jacobs, A. D.; Hoover, H.; Smith, E.; Clemmer, D. E., Kim, C.; Kao, C. The intrinsically disordered N-terminal arm of the brome mosaic virus coat protein specifically recognizes the RNA motif that directs the initiation of viral RNA replication, Nucleic Acids Research., 2017, 46, 324–335, DOI: 10.1093/nar/gkx1087
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  75. Masellis, C.; Khanal, N.; Kamrath, M. Z.; Clemmer, D. E.; Rizzo, T. R. Cryogenic Vibrational Spectroscopy Provides Unique Fingerprints for Glycan Identification, J. Am. Soc. Mass Spectrom., 2017, 10, 2217–2222, DOI: 10.1007/s13361-017-1728-6
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  76. Wagner, N.; Clemmer, D. E.; Russell, D. H. ESI-IM-MS and Collision-Induced Unfolding Provide Insight into the Linkage Dependent Interfacial Interactions of Covalently Linked Diubiquitin, Anal. Chem., 2017, 89, 10094–10103, DOI: 10.1021/acs.analchem.7b02932
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  77. Khanal, N.; Masellis, C.; Kamrath, M. Z.; Clemmer, D. E.; Rizzo, T. R. Glycosaminoglycan analysis by cryogenic messenger-tagging IR spectroscopy combined with IMS-MS, Anal. Chem., 2017, 89, 7601–7606, DOI: 10.1021/acs.analchem.7b01467
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  78. Sarbu, M.; Vukelic, Z.; Clemmer, D. E.; Zamfir, A. D. Electrospray ionization ion mobility mass spectrometry provides novel insights into the pattern and activity of fetal hippocampus gangliosides, Biochimie., 2017, 139, 81–94, DOI: 10.1016/j.biochi.2017.05.016
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  79. El-Baba, T. J.; Woodall, D. W.; Raab, S. A.; Fuller, D. R.; Laganowsky, A.; Russell, D. H.; Clemmer, D. E. Melting Proteins: Evidence for Multiple Stable Structures upon Thermal Denaturation of Native Ubiquitin from IMS-MS Measurements, J. Am. Chem. Soc., 2017, 139, 6306–6309, DOI: 10.1021/jacs.7b02774
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  80. Dilger, J. M.; Glover, M. S.; Clemmer, D. E. A Database of Transition-Metal-Coordinated Peptide Cross-Sections: Selective Interaction with Specific Amino Acid Residues, J. Am. Soc. Mass Spectrom., 2017, 28, 1293–1303, DOI: 10.1007/s13361-016-1592-9
    81. image
  81. Clemmer, D. E.; Russell, D. H.; Williams, E. R. Characterizing the Conformationome: Toward a Structural Understanding of the Proteome, Acc. Chem. Res., 2017, 50, 556–560, DOI: 10.1021/acs.accounts.6b00548
    82. image
  82. Kim, D.; Wagner, N.; Wooding, K.; Clemmer, D. E.; Russell, D. H. Ions from Solution to the Gas Phase: A Molecular Dynamics Simulation of the Structural Evolution of Substance P During Desolvation of Charged Nanodroplets Generated by Electrospray Ionization, J. Am. Chem. Soc., 2017, 139, 2981–2988, DOI:10.1021/jacs.6b10731
    83. image
  83. Musbat, L.; Nihamkin, M.; Toker, Y.; Dilger, J. M.; Fuller, D. R.; El-Baba, T. J.; Clemmer, D. E.; Sarkar, S.; Kronic, L.; Hirshfeld, A.; Friedman, N.; Sheves, M. Measurements of the stabilities of isolated retinal chromophores, Phys. Rev. E, 2017, 95, 012406-1–012406-7, DOI:10.1103/PhysRevE.95.012406
    84. image
  84. Gaye, M. M.; Ding, T.; Shion, H.; Hussein, A.; Hu, Y.; Zhou, S.; Hammoud, Z. T.; Lavine, B. K.; Mechref, Y.; Gebler, J. C.; Clemmer, D. E. Delineation of Disease Phenotypes Associated with Esophageal Adenocarcinoma by MALDI-IMS-MS Analysis of Serum N-linked Glycans, Analyst, 2017, 142, 1525–1535, DOI: 10.1039/C6AN02697D
    85. image
  85. Zhu, F.; Clemmer, D. E.; Trinidad, J. C. Characterization of lectin binding affinities via direct LC-MS profiling: implications for glycopeptide enrichment and separation strategies, Analyst, 2017, 142, 65–74, DOI:10.1039/C6AN02043G
    86. image

    Published:


    2016

  86. PATENT Clemmer, D. E.; Ewing, M. A.; Zucker, S. M.; Conant, C. R. Ion mobility spectrometer and method of operating same. US Pattent Office. 2016. US9368333B2
    87. image
  87. Rogers, D.; El-Baba, T. J.; Shi, L.; Khan, F.; Kim, D.; Hales, D. E.; Russel, D. E.; Clemmer, D. E. Histidine-modified polyproline-13 explores the nature of two-state cooperativity. Abs. Papers Amer. Chem. Soc. , 2016
  88. Clemmer, D. E. Pathways and thermodynamics of polyproline helix formation in solution from measurements of ions in the gas phase. Abs. Papers Amer. Chem. Soc. , 2016
  89. Fuller, D.; Clemmer, D. E. Developing IMS-MS technologies for analysis of peptide conformations and thermochemistry of binding in solution. Abs. Papers Amer. Chem. Soc. , 2016
  90. El-Baba, T. J.; Kim, D.; Rogers, D. B.; Khan, F. A.; Hales, D. A.; Russell, D. H.; Clemmer, D. E. Long-lived Intermediates in a Cooperative Two-State Folding Transition, J. Phys. Chem. B , 2016, 120, 12040–12046, DOI:10.1021/acs.jpcb.6b08932
    91. image
  91. Barr, J. D.; Shi, L.; Russell, D. H.; Clemmer, D. E.; Holliday, A. E. Following a Folding Transition with Capillary Electrophoresis and Ion Mobility Spectrometry, Anal. Chem., 2016, 88, 10933–10939, DOI:10.1021/acs.analchem.6b02424
    92. image
  92. Fuller, D.R.; Glover, M.S.; Pierson, N.A.; Kim, D.; Russell, D.H.; Clemmer, D.E. Cis→trans isomerization of Pro7 in Oxytocin regulates Zn2+ binding, J. Am. Soc. Mass. Spectrom., 2016, 27, 1–7, DOI:10.1007/s13361-016-1410-4
    93. image
  93. Voronina, L.; Masson, A.; Kamrath, M.; Schubert, F.; Clemmer, D. E.; Baldauf, C.; Rizzo, T. Conformations of prolyl-peptide bonds in the bradykinin 1-5 fragment in solution and in the gas phase, J. Am. Chem. Soc., 2016, 138, 9224–9233, DOI:10.1021/jacs.6b04550
    94. image
  94. Chatterjee, B.; Makarov, A.; Clemmer, D.E.; Steen, H.; Steen, J.; Saffell-Clemmer, W.; Moghekar, A. R.; Mohan Rao, C.; Bradshaw, R. A.; Thakur, S. S. Proteomics in India: A Report on Brainstorming Meeting at Hyderabad, India, Mol. Cell. Proteomics , 2016, DOI: 10.1074/mcp.O115.055020
    95. image
  95. Shi, L.; Holliday, A. E.; Bohrer, B. C.; Kim, D.; Servage, K. A.; Russell, D. H.; Clemmer, D. E. "Wet" Versus "Dry" Folding of Polyproline, J. Am. Soc. Mass Spectrom., 2016, 27, 1037–1047, DOI:10.1007/s13361-016-1343-y
    96. image
  96. Glover, M. S.; Dilger, J. M.; Acton, M. D.; Arnold, R. J.; Radivojac, P.; Clemmer, D. E. Examining the Influence of Phosphorylation on Peptide Ion Structure by Ion Mobility Spectrometry-Mass Spectrometry, J. Am. Soc. Mass Spectrom., 2016, 27, 786–794, DOI:10.1007/s13361-016-1343-y
    97. image
  97. Sarbu, M.; Robu, A. C.; Ghiulai, R.; Vukelic, Z.; Clemmer, D. E.; Zamfir, A. D. Electrospray ionization ion mobility mass spectrometry of human brain gangliosides, Anal. Chem., 2016, 88, 5166–6178, DOI:10.1021/acs.analchem.6b00155
    98. image
  98. Ewing, M. A.; Glover, M. S.; Clemmer, D. E. Hybrid Ion Mobility and Mass Spectrometry as a Separation Tool, Journal of Chromatography A , 2016, 1439, 3–25, DOI: 10.1016/j.chroma.2015.10.080
    99. image
  99. Gaye, M. M.; Nagy, G.; Clemmer, D. E.; Pohl, N. L. B. Multidimensional Analysis of 16 Glucose Isomers by Ion Mobility Spectrometry, Anal. Chem., 2016, 88, 2335–2334, DOI:10.1021/acs.analchem.5b04280
    100. image
  100. Shi, L.; Holliday, A. E.; Glover, M. S.; Ewing, M. A.; Russell, D. H.; Clemmer, D. E. Ion Mobility-Mass Spectrometry Reveals the Energetics of Intermediates that Guide Polyproline Folding, J. Am. Soc. Mass Spectrom. , 2016, 27, 22–30, DOI: 10.1007/s13361-015-1255-2
    101. image

    2015

  101. PATENT Clemmer, D. E.; Ewing, M. A.; Zucker, S. M.; Conant, C. R. Ion mobility spectrometer and method of operating same. US Pattent Office. 2015. US9129782B2
    102. image
  102. Servage, K. A.; Silveira, J. A.; Fort, K. L.; Clemmer, D.E., Russell, D. H. Water-Mediated Dimerization of Ubiquitin Ions Captured by Cryogenic Ion Mobility-Mass Spectrometry, J. Phys. Chem. Lett., 2015, 6, 4947–4951, DOI:10.1021/acs.jpclett.5b02382
    103. image
  103. Sarbu, M.; Zhu, F.; Peter-Katalinic, J.; Clemmer, D. E.; Zamfir, A. D. Application of Ion Mobility Tandem Mass Spectrometry To Compositional and Structural Analysis of Glycopeptides Extracted From The Urine of a Patient Diagnosed With Schindler Disease, Rapid Commun. Mass Spectrom, 2015, 29, 1929–1937, DOI: 10.1002/rcm.7288
    104. image
  104. Jacobs, A. D.; Chang, F. M.; Morrison, L.; Dilger, J. M.; Wysocki, V. H.; Clemmer, D. E.; Giedroc, D. P. Resolution of stepwise cooperativities of copper binding by the homotetrameric copper sensitive operon repressor (CsoR): Impact on structure and stability, Angew. Chem. Int. Ed. , 2015, 127, 12986–12990, DOI: 10.1002/anie.201506349
    105. image
  105. Masson, A.; Kamrath, M. Z.; Perez; M. A. S.; Glover, M. S.; Rothlisberger, U.; Clemmer, D. E.; Rizzo, T. R. Infrared spectroscopy of the mobility selected ions of H+ - Gly-Pro-Gly-Gly (GPGG), J. Am. Soc. Mass Spectrom., 2015, 26, 1444–1454
    106. image
  106. Lee, S.; Glover. M. S.; Reilly, J. P.; Clemmer, D. E. Photosynthesis of a Combinatorial Peptide Library in the Gas Phase, Anal. Chem., 2015, 87, 9384–9388, DOI: 10.1021/acs.analchem.5b02179
    107. image
  107. Khanal, N.; Pejaver, V.; Li, Z.; Radivojac, P.; Clemmer, D. E.; Mukhopadhyay, S. Position of Proline Mediates The Reactivity of S-palmitoylation, ACS Chem. Biol., 2015, 10, 2529–2536, DOI:10.1021/acschembio.5b00429
    108. image
  108. Snijder, J.; Waterbeemd, M.; Glover, M. S.; Shi, L.; Clemmer, D. E.; Heck, J. R. Conformational landscape and pathway of disulfide bond reduction of human alpha defensin, Protein Science, 2015, 24, 1264–1271, DOI:10.1002/pro.2694
    109. image
  109. Glover, M. S.; Bellinger, E. P.; Radivojac, P.; Clemmer, D. E. Penultimate Proline in Neuropeptides, Anal. Chem., 2015, 87, 8466–8472, DOI: 10.1021/acs.analchem.5b01889
    110. image
  110. Servage, K. A.; Fort, K.; Silveira, J.; Shi, L.; Clemmer, D. E.; Russell, D. H. Unfolding of Hydrated Alkyl Diammonium Cations Revealed by Cryogenic Ion Mobility-Mass Spectrometry, J. Am. Chem. Soc., 2015, 137, 8916–8919, DOI: 10.1021/jacs.5b05448
    111. image
  111. Shi, L.; Holliday, A. E.; Khanal, N.; Russell, D. H.; Clemmer, D. E. Configurationally-Coupled Protonation of Polyproline-7, J. Am. Chem. Soc., 2015, 137, 8680–8683, DOI: 10.1021/jacs.5b04287
    112. image
  112. Zhu, F.; Trinidad, J. C.; Clemmer, D. E. Glycopeptide Site Heterogeneity and Structural Diversity Determined by Combined Lectin Affinity Chromatography/IMS/CID/MS Techniques, J. Am. Soc. Mass Spectrom., 2015, 26, 1092–1102
    113. image
  113. Ewing, M. A.; Conant, C. R. P.; Zucker, S. M.; Griffith, K. J.; Clemmer, D. E. Selected Overtone Mobility Spectrometry, Anal. Chem., 2015, 87, 5132–5138.
    114. image
  114. Dilger, J.; Musbat, L.; Sheves, M.; Bochenkova, A. V.; Clemmer, D. E., Toker, Y. Direct Measurement of the Isomerization Barrier of the Isolated Retinal Chromophore, Angew. Chem. Int. Ed., 2015, 54, 1–6.
    115. image
  115. Glover, M. S.; Shi, L.; Fuller, D. R.; Arnold, R. J.; Radivojac, P.; Clemmer, D. E. On the Split Personality of Penultimate Proline, J. Am. Soc. Mass Spectrom., 2015, 26, 444–452.
    116. image
  116. Pierson, N. A.; Clemmer. D. E. An IMS-IMS threshold method for semi-quantitative determination of activation barriers: Interconversion of proline cis↔trans forms in triply protonated bradykinin, Int. J. Mass Spectrom., 2015, 377, 646–654.
    117. image
  117. Gaye, M. M.; Kurulugama, R; Clemmer, D. E. Investigating Carbohydrate Isomers by IMS-CID-IMS-MS: Precursor and Fragment Ion Cross-sections, Analyst , 2015, 140, 6922–6932, DOI:10.1039/C5AN00840A
    118. image
  118. Larriba-Andaluz, C.; Fernandez-Garcia, J.; Ewing, M. A.; Hogan, C. J.; Clemmer, D. E. Gas Molecule Scattering & Ion Mobility Measurements for Organic Macro-ions in He versus N2 Environments, Phys. Chem. Chem. Phys., 2015, 17, 15019–15029
    119. image
  119. Zhu, F.; Glover, M. S.; Shi, H.; Trinidad, J. C.; Clemmer. D. E. Populations of Metal-Glycan Structures Influence MS Fragmentation Patterns, J. Am. Soc. Mass Spectrom., 2015, 26, 25–35.
    120. image

    2014

  120. PATENT Clemmer, D. E.; Ewing, M. A.; Zucker, S. M.; Conant, C. R. Ion mobility spectrometer and method of operating same. US Pattent Office. 2014. US8872102B2
    121. image
  121. Shi, H.; Atlasevich, N.; Merenbloom, S. I.; Clemmer. D. E. Solution Dependence of the Collisional Activation of Ubiquitin [M+7H]7+ Ions, J. Am. Soc. Mass Spectrom. , 2014, 25, 2000–2008.
    122. image
  122. Fort, K. L.; Silveira, J. A.; Pierson, N. A.; Servage, K. A.; Clemmer, D. E.; Russell, D. H. From Solution to the Gas Phase: Factors That Influence Kinetic Trapping of Substance P in the Gas Phase, J. Phys. Chem. B, 2014, 118, 14336–14344.
    123. image
  123. Shi, L.; Holliday, A. E.; Shi, H.; Zhu, F.; Ewing, M. A.; Russell, D. H.; Clemmer. D. E. Characterizing Intermediates along the Transition from Polyproline I to Polyproline II using Ion Mobility Spectrometry-Mass Spectrometry, J. Am. Chem. Soc., 2014, 136, 12702–12711.
    124. image
  124. Larriba, C.; Fernandez de la Mora, J.; Clemmer. D. E. Electrospray Ionization Mechanisms for Large Polyethylene Glycol Chains studied through Tandem Ion Mobility Spectrometry, J. Am. Soc. Mass Spectrom., 2014, 25, 1332–1345.
    125. image
  125. Li, Z.; Dilger, J. M.; Pejaver, V.; Smiley, D.; Arnold, R. J.; Mooney, S. D.; Mukhopadhyay, S.; Radivojac, P.; Clemmer. D. E. Intrinsic Size Parameters for Palmitoylated and Carboxyamidomethylated Peptides, Int. J. Mass Spectrom., 2014, 368, 6–14.
    126. image
  126. Wyttenbach, T.; Pierson, N. A.; Clemmer. D. E.; Bowers, M. T. Ion Mobility Analysis of Molecular Dynamics, Annu. Rev. Phys. Chem. , 2014, 65, 175–196.
    127. image
  127. Shi, H.; Clemmer. D. E. Evidence for Two New Solution States of Ubiquitin by IMS-MS Analysis, J. Phys. Chem. B, 2014, 118, 3498–3506.
    128. image
  128. Johnson, A. R.; Dilger, J. M.; Glover, M. S.; Clemmer. D. E., Carlson, E. E. Negatively-Charged Helices in the Gas Phase, Chem. Comm., 2014, 50, 8849–8851.
    129. image

    2013

  129. PATENT Clemmer, D. E.; Koeniger, S. L.; VAlentine, S. J. Ion mobility spectrometer with one or more integral ion activation regions . US Pattent Office. 2013. US8618475B2
    130. image
  130. PATENT Clemmer, D. E.; Kurulugama, R. T.; Nachtigall, F. M.; Henson, Z.; Merenbloom, S. I.; Valentine, S. J. Ion mobility spectrometer instrument and method of operation. US Pattent Office. 2013. US8513591B2
    131. image
  131. PATENT Clemmer, D. E.; Merenbloom, S. I.; Koeniger, S. L.; Valentine, S. J. Apparatus and methods for analyzing ions . US Pattent Office. 2013. US8362420B2
    132. image
  132. Silveira, J. A.; Fort, K. L.; Pierson, N. A.; Clemmer, D. E.; Russell, D. H. From Solution to the Gas Phase: Stepwise Dehydration and Kinetic Trapping of Substance P Reveals the Origin of Peptide Conformations, J. Am. Chem. Soc., 2013, 135, 19147–19153.
    133. image
  133. Glover, M. S.; Dilger, J. M.; Zhu, F.; Clemmer, D. E. The Binding of Ca2+, Co2+, Ni2+, Cu2+, and Zn2+ Cations to Angiotensin I Determined by Mass Spectrometry based Techniques, Int. J. Mass Spectrom., 2013, 354-355, 318–325.
    134. image
  134. Zucker, S. M.; Ewing, M. A.; Clemmer, D. E. Gridless Overtone Mobility Spectrometry, Anal. Chem., 2013, 85,10174–10179.
    135. image
  135. Glaskin, R. S.; Ewing, M. A.; Clemmer, D. E. Ion Trapping for Ion Mobility Spectrometry Measurements in a Cyclical Drift Tube, Anal. Chem., 2013, 85, 7003–7008.
    136. image
  136. Dilger, J. M.; Valentine, S. J.; Glover, M. S; Clemmer, D. E. A Database of Alkaline-earth-coordinated Peptide Cross Sections: Insights into General Aspects of Structure. J. Am. Soc. Mass Spectrom., 2013, 24, 768–779.
    137. image
  137. Ewing, M. A.; Zucker, S. M.; Valentine, S. J.; Clemmer, D. E. Overtone Mobility Spectrometry: Part 5. Simulations and Analytical Expressions Describing Overtone Limits. J. Am. Soc. Mass Spectrom., 2013, 24, 615–621.
    138. image
  138. Pierson, N. A.; Chen, L.; Russell, D. H.; Clemmer, D. E. Cis–Trans Isomerizations of Proline Residues are Key to Bradykinin Conformations. J. Am. Chem. Soc., 2013, 135, 3186–3192.
    139. image
  139. Shi, H.; Gu, L.; Clemmer, D. E.; Robinson, R. A. S. Effects of Fe(II)/H2O2 Oxidation on Ubiquitin Conformers Measured by Ion Mobility-Mass Spectrometry. J. Phys. Chem. B, 2013, 117, 164–173.
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    140. 2012

  140. Dilger, J. M.; Valentine, S. J.; Glover, M. S.; Ewing, M. A.; Clemmer, D. E. A Database of Alkali Metal-Containing Peptide Cross Sections: Influence of Metals on Size Parameters for Specific Amino Acids. Int. J. Mass Spectrom., 2012, 330-332, 35–45.
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  141. Rodgers, M. T.; Clemmer, D. E. A celebration of the scientific and personal contributions of Peter B. Armentrout. Int. J. Mass Spectrom., 2012, 330-332, 4–5.
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  142. Rodgers, M. T.; Clemmer, D. E. An Appreciation. Int. J. Mass Spectrom., 2012, 330-332, 2–3.
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  143. Gaye, M. M.; Valentine, S. J.; Hu, Y.; Mirjankar, N.; Hammoud, Z. T.; Mechref, Y.; Lavine, B. K.; Clemmer, D. E. Ion Mobility-Mass Spectrometry Analysis of Serum N-Linked Glycans from Esophageal Adenocarcinoma Phenotypes. J. Prot. Res., 2012, 11, 6102–6110.
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  144. Zhu, F.; Lee, S.; Valentine, S. J.; Reilly, J. P.; Clemmer, D. E. Mannose7 Glycan Isomer Characterization by IMS-MS/MS Analysis. J. Am. Soc. Mass Spectrom., 2012, 23, 2158–2166.
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  145. Atlasevich, N.; Holliday, A.; Valentine, S. J.; Clemmer, D. E. Chirality and Packing in Small Proline Clusters. J. Phys. Chem. B, 2012, 116, 11442–11446.
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  146. Holliday, A.; Atlasevich, N.; Myung, S.; Plasencia, M. D.; Valentine, S. J.; Clemmer, D. E. Oscillations for Chiral Preference in Proline Clusters. J. Phys. Chem. A., 2013, 117, 1035–1041.(Special Issue in honor of Peter B. Armentrout Festschrift)
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  147. Atlasevich, N.; Holliday, A.; Valentine, S. J.; Clemmer, D. E. Collisional Activation of [14Pro+2H]2+ Clusters: Chiral Dependence of Evaporation and Fission Processes. J. Phys. Chem. B., 2012, 116, 7644–7651.
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  148. Lee, S.; Julian, R. R.; Valentine, S. J.; Reilly, J. P., Clemmer, D. E. Biomolecular condensation via ultraviolet excitation in vacuo. Int. J. Mass Spectrom., 2012, 316–318, 6–11.
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  149. Shi, H.; Pierson, N. A.; Valentine, S. J.; 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. J. Phys. Chem. B, 2012, 116, 3344–3352.
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  150. 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. 2012, 11, 576–585.
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  151. Lee, S.; Valentine, S. J.; Reilly, J. P.; Clemmer, D. E. Analyzing a Mixture of Disaccharides by IMS–VUVPD–MS. Int. J. Mass Spectrom., 2012, 309, 161–167.
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  152. Lee, S.; Li, Z.; 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. Int. J. Mass Spectrom., 2012, 309, 154–160.
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    153. 2011

  153. 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, 22, 2049–2060.
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  154. 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, 15834–15837.
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  155. 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, 13810–13813.
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  156. 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, 1602–1609.
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  157. 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, 1477–1485.
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  158. 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.
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  159. 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. Anal. Chem., 2011, 83, 5377–5385.
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  160. 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, 2318–2329.
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  161. 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, 804–16.
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  162. 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, 817–27.
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  163. Bohrer, B. C.; Atlasevich, N.; Clemmer, D. E. Transitions between Elongated Conformations of Ubiquitin [M+11H]11+ Enhance Hydrogen/Deuterium Exchange. J. Phys. Chem. B 2011, 115, 4509–4515.
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    164. 2010

  164. PATENT Clemmer, D. E.; Kurulugama, R. T.; Nachtigall, F. M.; Henson, Z.; Merenbloom, S. I.; Valentine, S. J. Ion mobility spectrometer instrument and method of operating same. US Pattent Office. 2010. US7838821B2
    165. image
  165. Bohrer, B. C.; Li, Y. F.; Reilly, J. P.; Clemmer, D. E.; Di Marchi, R. D.; Radivojac, P.; Tang, H.; Arnold, R. J. Combinatorial Libraries of Synthetic Peptides as a Model for Shotgun Proteomics. Anal. Chem. 2010, 82, 6559–6568.
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  166. Kim, T.-Y.; Valentine, S. J.; Clemmer, D. E.; Reilly, J. P. Gas-Phase Conformation-Specific Photofragmentation of Proline-Containing Peptide Ions. J. Am. Soc. Mass Spectrom. 2010, 21, 1455–1465.
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  167. Trimpin, S.; Clemmer, D. E.; and Larsen, B. S. Snapshot, Conformation, and Bulk Fragmentation of Polymeric Architectures using ESI–IMS–MS, in Ion Mobility Spectrometry–Mass Spectrometry: Theory and Applications, CRC Press:2010, 215–235.
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  168. Glaskin, R. S.; Valentine, S. J.; Clemmer, D. E. A Scanning Frequency Mode for Ion Cyclotron Mobility Spectrometry. Anal. Chem. 2010, 82, 8266–8271.
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  169. Shvartsburg, A. A.; Clemmer, D. E.; Smith, R. D. Isotopic Effect on Ion Mobility and Separation of Isotopomers by High-Field Ion Mobility Spectrometry. Anal. Chem. 2010, 82, 8047–8051.
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  170. Lee, S.; Ewing, M. A.; Nachtigall, F. M.; Kurulugama, R. T.; Valentine, S. J.; Clemmer, D. E. Determination of Cross Sections by Overtone Mobility Spectrometry: Evidence for Loss of Unstable Structures at Higher Overtones. J. Phys. Chem. B 2010, 114, 12406–12415.
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  171. Robinson, R. A. S.; Kellie, J. F.; Kaufman, T. C.; Clemmer, D. E. Insights into aging through measurements of the Drosophila proteome as a function of temperature. Mechanisms of Ageing and Development 2010, 131, 584–590.
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  172. [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, 2010, 191 [Ref 137: 19, 2008, 1706–1715].
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  173. Pierson, N. A.; Valentine, S. J.; Clemmer, D. E. 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.
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  174. 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, 2852–2860.
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    175. 2009

  175. 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, 4500–4510.
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  176. Valentine, S. J.; Clemmer, D. E. Protein oligomers frozen in time. Nature Chemistry 2009, 1, 257–258.
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  177. Valentine, S. J.; Clemmer, D. E. Treatise on the Measurement of Molecular Masses with Ion Mobility Spectrometry. Anal. Chem. 2009, 81, 5876–5880.
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  178. 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. Int. J. Mass Spectrom. 2009, 287, 58–69.
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  179. 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. Int. J. Mass Spectrom. 2009 283, 149–160.
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  180. Merenbloom, S. I.; Glaskin, R. S.; Henson, Z. B.; Clemmer, D. E. High-Resolution Ion Cyclotron Mobility Spectrometry. Anal. Chem. 2009, 81, 1482–1487.
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  181. Valentine, S. J.; Stokes, S. T.; Kurulugama, R.; Nachtigall, F. M.; Clemmer, D. E. Overtone Mobility Spectrometry (Part 2): Theoretical Considerations of Resolving Power. J. Am. Soc. Mass Spectrom. 2009, 20, 738–750.
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  182. Kurulugama, R., Nachtigall, F. M., Lee, S., Valentine, S. J., Clemmer, D. E. Overtone Mobility Spectrometry (Part 1): Experimental Observations. J. Am. Soc. Mass Spectrom. 2009, 20, 729–737.
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    183. 2008

  183. Xun, Z.; Kaufman, T. C.; Clemmer, D. E. Proteome response to the panneural expression of human wild-Type α-Synuclein: a Drosophila Model of Parkinson’s Disease. J. Proteome Res. 2008, 7, 3911–3921.
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  184. Trimpin, S.; Clemmer, D. E. Ion Mobility Spectrometry/Mass Spectrometry Snapshots for Assessing the Molecular Compositions of Complex Polymeric Systems. Anal. Chem., 2008, 80, 9073–9083.
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  185. 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, 1706–1715.
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  186. 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, 318–331.
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  187. Xun, Z.; Sowell, R. A.; Kaufman, T. C.; Clemmer, D. E. Quantitative Proteomics of a Presymptomatic A53T α-Synuclein Drosophila Model of Parkinson Disease. Mol. Cell. Proteomics, 2008, 7, 1191–1203.
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  188. 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, 102–109.
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  189. 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. Anal. Chem. 2008, 80, 1918–1927.
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  190. 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.
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  191. 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, 1109–1117.
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  192. Bohrer, B. C.; Merenbloom, S. I.; Koeniger, S. L.; Hilderbrand, A. E.; Clemmer, D. E. Biomolecule Analysis by Ion Mobility Spectrometry, Annu. Rev. Anal. Chem., 2008, 1, 293–327.
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    193. 2007

  193. PATENT Clemmer, D. E.; Koeniger, S.; Valentine, S. Ion mobility spectrometer . US Pattent Office. 2007. US20070114382A1
    194. image
  194. 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.
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  195. 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.
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  196. 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.
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  197. 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.
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  198. 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]
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  199. Trimpin, S.; Plasencia, M.; Isailovic, D.; Clemmer, D. E. Resolving Oligomers from Fully Grown Polymers with IMS–MS, Anal. Chem. 2007, 79, 7965–7974.
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  200. 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.
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  201. 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, Anal. Chem. 2007, 79, 515–522. [Cover Image]
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  202. Koeniger, S. L.; Clemmer, D. E.Resolution and Structural Transitions of Elongated States of Ubiquitin. J. Am. Soc. Mass Spectrom. 2007, 18, 322–331.
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    203. 2006

  203. PATENT Clemmer, D. E. Instrument for separating ions in time as functions of preselected ion mobility and ion mass . US Pattent Office. 2006. US7077944B2
    204. image
  204. 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.
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  205. 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.
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  206. 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.
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  207. 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.
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  208. Hilderbrand, A. E.; Myung, S.; Clemmer, D. E. Exploring Crown Ethers as Shift Reagents for Ion Mobility Spectrometry, Anal. Chem. 2006, 78, 6792–6800.
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  209. 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.
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  210. 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.
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  211. 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, Anal. Chem. 2006, 78, 4161–4174.
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  212. 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.
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  213. 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, Anal. Chem. 2006, 78, 2802–2809.
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  214. 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.
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  215. Myung, S.; Wiseman, J. M.; Valentine, S. J.; Zolt�n, 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.
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    216. 2005

  216. PATENT Clemmer, D. E. Instrument for separating ions in time as functions of preselected ion mobility and ion mass. US Pattent Office. 2005. US6960761B2
    217. image
  217. 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.
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  218. 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.
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  219. 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.
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  220. 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.
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  221. Myung, S.; Pink, M.; Baik, M.; Clemmer, D. E. DL–Proline, Acta Cryst. 2005, C61, 506–508.
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  222. 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.
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  223. 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.
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  224. Julian, R. R.; Myung, S.; Clemmer, D. E. Do Homochiral Aggregates Have an Entropic Advantage? J. Phys. Chem. B 2005, 109, 440–444.
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  225. 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.
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    226. 2004

  226. 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.
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  227. 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.
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  228. 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.
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  229. 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.
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  230. Julian, R. R.; Myung, S.; Clemmer, D. E. Spontaneous Anti-Resolution in Heterochiral Clusters of Serine,J. Am. Chem. Soc. 2004, 126, 4110–4111.
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  231. Counterman, A. E.; Clemmer, D. E. Anhydrous Polyproline Helices and Globules, J. Phys. Chem. B 2004, 108, 4885–4898.
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    232. 2003

  232. 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.
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  233. 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.
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  234. 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]
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  235. 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.
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  236. Valentine, S. J.; Koeniger, S. L.; Clemmer, D. E. A Split-field Drift Tube for Separation and Efficient Fragmentation of Biomolecular Ions, Anal. Chem. 2003, 75, 6202–6208.
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  237. Myung, S.; Lee, Y. J.; 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. A.; 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, Anal. Chem. 2003, 75, 5137–5145.
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  238. Hilderbrand, A. E.; Valentine, S. J.; Clemmer, D. E. Mobilities: Biological Systems and Clusters in Encyclopedia of Mass Spectrometry Volume 1: Theory and Ion Chemistry; Gross, M. L.; Caprioli, R. and Armentrout, P., Eds.; Elsevier: Kidlington, Oxford, 2003, p.506–520.
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  239. 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, Anal. Chem. 2003, 75, 1684–1690.
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  240. Counterman, A. E.; Clemmer, D. E. Compact → Extended Helix Transitions of Polyalanine in Vacuo, J. Phys. Chem. B 2003, 107, 2111–2117.
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  241. 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.
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    242. 2002

  242. PATENT Clemmer, D. E. Ion Separation Instrument. US Pattent Office. 2002. US6498342B1
    243. image
  243. 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]
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  244. Counterman, A. E.; Clemmer, D. E. Gas Phase Polyalanine: Assessment of i→i+3 and i→i+4 Helical Turns in [Alan+4H]4+ (n = 29–49) Ion, J. Phys. Chem. B 2002, 106, 12045–12051.
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  245. 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 60th birthday]
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  246. 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, Anal. Chem. 2002, 74, 4889–4894.
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  247. 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.
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  248. 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.
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  249. Counterman, A. E.; Clemmer, D. E. Cis–Trans Signatures of Proline-Containing Tryptic Peptides in the Gas Phase, Anal. Chem. 2002, 74, 1946–1951.
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  250. 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.
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  251. 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, Anal. Chem. 2002, 74, 1360–1370.
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  252. 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, Anal. Chem. 2002, 74, 992–1006.
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  253. 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, Anal. Chem. 2002, 74, 950–958.
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  254. 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, Anal. Chem. 2002, 74, 26–36.
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    255. 2001

  255. PATENT Clemmer, D. E.; Reilly, J. P. Ion mobility and mass spetrometer. US Pattent Office. 2001. US6323482B1
    256. image
  256. 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]
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  257. 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, Anal. Chem. 2001, 73, 6000–6007.
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  258. Counterman, A. E.; Clemmer, D. E. Magic Number Clusters of Serine in the Gas Phase, J. Phys. Chem. B 2001, 105, 8092–8096.
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  259. 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, Anal. Chem. 2001, 73, 3549–3555.
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  260. 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.
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  261. 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.
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  262. 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.
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  263. 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.
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  264. Taraszka, J. A.; Counterman, A. E.; Clemmer, D. E. Gas–Phase separations of complex tryptic peptide mixtures, Fresenius J. Anal. Chem., 2001, 369, 234–245.
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  265. 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.
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  266. 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.
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  267. 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, Anal. Chem. 2001, 73, 424–433.
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  268. Hoaglund-Hyzer, C. S.; Clemmer, D. E. Ion Trap/Ion Mobility/Quadrupole/Time-of-Flight Mass Spectrometry for Peptide Mixture Analysis, Anal. Chem. 2001, 73, 177–184.
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    269. 2000

  269. PATENT Sporleder, C. R.; Clemmer, D. E. Electric field generation for charged particle analyzers. US Pattent Office. 2000. US6040573A
    270. image
  270. Hoaglund-Hyzer, C. S.; Li, J.; Clemmer, D. E. Mobility Labeling for Parallel CID of Ion Mixtures, Anal. Chem. 2000, 72, 2737–2740.
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  271. 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.
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  272. 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.
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    273. 1999

  273. PATENT Clemmer, D. E.; Reilly, J. P. Hybrid ion mobility and mass spectrometer. US Pattent Office. 1999. US5905258A
    274. image
  274. 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.
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  275. Hoaglund-Hyzer, C. S.; Counterman, A. E.; Clemmer, D. E. Anhydrous Protein Ions, Chem. Rev. 1999, 99, 3037–3079.
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  276. 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.
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  277. Srebalus, C. A.; Li, J.; Marshall, W. S.; Clemmer, D. E. Gas-Phase Separations of Electrosprayed Peptide Libraries, Anal. Chem. 1999, 71, 3918–3927.
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  278. 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.
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  279. 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.
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  280. 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, Anal. Chem. 1999, 71, 291–301.
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    281. 1998

  281. 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.
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  282. 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.
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  283. Hoaglund, C. S.; Valentine, S. J.; Sporleder, C. R.; Reilly, J. P.; Clemmer, D. E. Three-Dimensional Ion Mobility/TOFMS Analysis of Electrosprayed Biomolecules, Anal. Chem. 1998, 70, 2236–2242.
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  284. 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.
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    285. 1997

  285. 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.
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  286. Hoaglund, C. S.; Valentine, S. J.; Clemmer, D. E. An Ion Trap Interface for ESI–Ion Mobility Experiments, Anal. Chem. 1997, 69, 4156–4161.
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  287. Liu, Y.; Valentine, S. J.; Counterman, A. E.; Hoaglund, C. S.; Clemmer, D. E. Injected–ion Mobility Analysis of Biomolecules, Anal. Chem. 1997, 69, 728A.
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  288. 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.
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  289. Liu, Y.; Clemmer, D. E. Characterizing Oligosaccharides Using Injected–Ion Mobility/Mass Spectrometry, Anal. Chem. 1997, 69, 2504–2509.
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  290. Clemmer, D. E.; Jarrold, M. F. Ion Mobility Measurements and their Applications to Clusters and Biomolecules, J. Mass Spectrom. 1997, 32, 577–592.
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  291. 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.
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  292. 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.
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  293. 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.
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  294. Dugourd, P.; Hudgins, R. R.; Clemmer, D. E.; Jarrold, M. F. High-resolution ion mobility measurements, Rev. Sci. Instrum. 1997, 68, 1122–1129.
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  295. 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.
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    296. 1996

  296. Shelimov, K. B.; Clemmer, D. E.; Jarrold, M. F. Metal Containing Carbon Clusters, J. Chem. Soc. Dalton Trans. 1996, 567–574.
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  297. 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.

    298. 1995

  298. 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.
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  299. 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.
  300. Shelimov, K. B.; Clemmer, D. E.; Jarrold, M. F. Structures and Isomerization of LaCn+ Clusters, J. Phys. Chem. 1995, 99, 11376–11386.
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  301. Clemmer, D. E.; Jarrold, M. F. Metal-Containing Carbon Clusters: Structures, Isomerization, and Formation of NbCn+ Clusters, J. Am. Chem. Soc. 1995, 117, 8841–8850.
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    302. 1994

  302. 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.
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  303. 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.
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  304. Shelimov, K. B.; Clemmer, D. E.; Jarrold, M. F. Structures and Formation of Small LaCn+ Metallofullerenes, J. Phys. Chem. 1994, 98, 12819–12821.
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  305. 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.
  306. 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.
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  307. 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.
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  308. Clemmer, D. E.; Shelimov, K. B.; Jarrold, M. F. Bonding of Metals to Carbon Rings: LaCn+ Isomers with La+ Inserted and Attached to the Ring, J. Am. Chem. Soc. 1994, 116, 5971–5972.
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  309. 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.
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  310. 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.
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  311. 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.
  312. Clemmer, D. E.; Shelimov, K. B.; Jarrold, M. F. Gas-Phase Self-Assembly of Endohedral Metallofullerenes, Nature 1994, 367, 718–720.
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    313. 1993

  313. 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.
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  314. 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.
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  315. Chen, Y. M.; Clemmer, D. E.; Armentrout, P. B. Gas-phase thermochemistry of VH and CrH, J. Chem. Phys. 1993, 98, 4929–4936.
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  316. 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.
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    317. 1992

  317. 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.
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  318. 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.
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  319. 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.
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  320. 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.
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    321. 1991

  321. 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.
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  322. 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.
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  323. Chen, Y.M.; Clemmer, D. E.; Armentrout, P. B. The gas-phase thermochemistry of TiH, J. Chem. Phys. 1991, 95, 1228–1233.
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  324. 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.
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    325. 1990

  325. 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.
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  326. 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.
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  327. 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.
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    328. 1989

  328. Clemmer, D. E.; Armentrout, P. B.; Investigation of Isomeric Intermediates: Co+–NH3 and H–Co+–NH2, J. Am. Chem. Soc. 1989, 111, 8280–8281.
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