The overall thrust of this research initiative is to develop new and improved means for manipulating and interrogating macro-molecular ions with strong emphasis on polypeptide species, including peptides derived from enzymatic or chemical digestion, whole proteins, and protein complexes. The ultimate objective is to maximize the structural information that can be derived from proteins and protein complexes of interest for the purpose of their identification and characterization. The work involves emphases in ion formation, ion chemistry, and instrumentation pertinent to mass spectrometry and tandem mass spectrometry. Gas-phase ions serve as surrogates for the condensed-phase species of interest. Structural information in tandem mass spectrometry is derived both from ion chemistry and the accurate measurement of the masses of the charged reaction products. The nature of the ion (e.g., protonated molecule versus radical cation) plays a major role in its chemistry, as do the reaction conditions. This research is based on the premise that new ion chemistries, new tools, and new methodologies can address many of the current limitations in the ability of mass spectrometry to derive structural information from large polypeptide species. It is also based on the premise that it is both desirable and possible to separate the ionization process from the ion manipulation/interrogation and mass analysis steps so that each can be optimized individually. To further increase the protein structural information accessible from mass spectrometry and tandem mass spectrometry, we propose the following specific aims:
Specific Aim 1 : New and improved ion chemistry-based approaches for protein identification and structural characterization.
Specific Aim 2 : New instrumentation and methodologies for tandem mass spectrometry of peptides and proteins in "hybrid" tandem mass spectrometers.
Specific Aim 3 : Development of novel approaches for tandem mass spectrometry of proteins ionized via matrix-assisted laser desorption ionization (MALDI).
These aims will be met by the development of novel ion/ion reactions for ion transformation, an expanded range of ion activation methods, instrument development to support the new ion chemistries, and the development of new approaches to protein identification/characterization that are enabled by the advances in ion chemistry and instrumentation.

Public Health Relevance

This project is directed at improved protein identification/characterization. The ability to identify a protein and to characterize its post-translational modifications (i.e., identities and locations of modifications) underlie much of fundamental biomedical research. This capability is also key to the identification of protein biomarkers and their correlation with disease. This project seeks to address this task by greatly expanding the information content accessible via mass spectrometry.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Enabling Bioanalytical and Biophysical Technologies Study Section (EBT)
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Edmonds, Charles G
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Purdue University
Schools of Arts and Sciences
West Lafayette
United States
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McGee, William M; McLuckey, Scott A (2014) Efficient and directed peptide bond formation in the gas phase via ion/ion reactions. Proc Natl Acad Sci U S A 111:1288-92
Pilo, Alice L; McLuckey, Scott A (2014) Oxidation of methionine residues in polypeptide ions via gas-phase ion/ion chemistry. J Am Soc Mass Spectrom 25:1049-57
Prentice, Boone M; Stutzman, John R; McLuckey, Scott A (2013) Reagent cluster anions for multiple gas-phase covalent modifications of peptide and protein cations. J Am Soc Mass Spectrom 24:1045-52
Mentinova, Marija; Crizer, David M; Baba, Takashi et al. (2013) Cation recombination energy/coulomb repulsion effects in ETD/ECD as revealed by variation of charge per residue at fixed total charge. J Am Soc Mass Spectrom 24:1676-89
Prentice, Boone M; Gilbert, Joshua D; Stutzman, John R et al. (2013) Gas-phase reactivity of carboxylic acid functional groups with carbodiimides. J Am Soc Mass Spectrom 24:30-7
Stutzman, John R; Blanksby, Stephen J; McLuckey, Scott A (2013) Gas-phase transformation of phosphatidylcholine cations to structurally informative anions via ion/ion chemistry. Anal Chem 85:3752-7
Webb, Ian K; Mentinova, Marija; McGee, William M et al. (2013) Gas-phase intramolecular protein crosslinking via ion/ion reactions: ubiquitin and a homobifunctional sulfo-NHS ester. J Am Soc Mass Spectrom 24:733-43
McGee, William M; McLuckey, Scott A (2013) The ornithine effect in peptide cation dissociation. J Mass Spectrom 48:856-61
Webb, Ian K; Gao, Yang; Londry, Frank A et al. (2013) Trapping mode dipolar DC collisional activation in the RF-only ion guide of a linear ion trap/time-of-flight instrument for gaseous bio-ion declustering. J Mass Spectrom 48:1059-65
Prentice, Boone M; McGee, William M; Stutzman, John R et al. (2013) Strategies for the Gas Phase Modification of Cationized Arginine via Ion/ion Reactions. Int J Mass Spectrom 354-355:

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