Carolyn J. Cassady - US grants

The gas-phase chemistry of multiply charged protein ions generated by electrospray ionization mass spectrometry will be investigated. Ion/molecule reactions ad dissociation techniques will be used to obtain structural information on high mass biological ions. Fundamental kinetic, thermodynamic, and mechanistic aspects of these processes will also be considered. The development of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR or FTMS) as a tool for studies of ions generated by electrospray is an additional goal of this research. Reactivity studies will center on proton transfer and hydrogen/deuterium exchange. The effect of the gas-phase basicity of the neutral reaction partner on product formation and kinetics will be investigated. Proton transfer reactions will also include anionic partners. The impact of a protein's structure on its reactivity will be explored by varying the molecular weight of the protein, the number of protons in the ion, the basicities of the amino acid residues present, the sequence of residues, and the conformation of the ions. Multiply protonated protein ions will be subjected to low-energy collision-induced dissociation (CID) experiments. These studies will provide knowledge of the effects of protein structure on dissociation patterns. A goal is to determine which charge states, or combinations of charge states, provide the most informative fragmentation. A wide range of charge states will be investigated. Proton transfer reactions will be used to lower the degree of protonation for some proteins. Where possible, comparisons will be made between the CID pathways of multiply charged ions and those of singly charged ions produced by fast atom bombardment (FAB). The effect of experimental parameters on the spectra will be considered, with single and multiple collision conditions and sustained off-resonance irradiation being explored. Studies of both native and denaturized proteins will be performed to establish the influence of conformational features on the CID spectra. In addition, electron-induced dissociation (EID) will be evaluated as an alternative to CID for obtaining structural information on multiply charged protein ions.

The objective of this research is to develop procedures for the analysis of acidic peptides by negative ion mass spectrometry. Many biological peptides and peptides used in disease treatment have numerous glutamic or aspartic acid residues; others contain acidic phosphate or sulfate groups. In the past fifteen years, advances in mass spectrometry have made it a method of choice for determining the molecular masses and sequences of peptides. Hundreds of reports have appeared on the tandem mass spectrometry (MS/MS) of positively-charged, protonated peptide ions. In contrast, relatively little work has focused on negatively- charged, deprotonated ions and the majority of these studies have dealt with singly charged ions containing four or fewer residues. However, acidic peptides often form negative ions more readily than positive ions. This project will utilize two advancing methodologies in mass spectrometry: electrospray ionization Fourier transform ion cyclotron resonance (ESI/FT-ICR) and matrix-assisted laser desorption ionization time-of-flight (MALDI/TOF). ESI/FT-ICR studies will involve low-energy collision-induced dissociation (CID) on multiply deprotonated ions, while MALDI/TOF work will employ post-source decay (PSD) on singly deprotonated ions. The major aim is to elucidate dissociation mechanisms. Fragmentations induced by various types of amino acid residues and by their sequences will be explored. Structural features under investigation include glutamic and aspartic acid residue, non- acidic residues such a proline and lysine, the C-terminal endgroup (-OH or NH2), highly acidic phosphate and sulfate groups, and interactions between acidic and basic residues. For multiply deprotonated ions generated by ESI, the number and locations of ionic charges (and thus the magnitude of Coulomb repulsion) must be considered. Molecular dynamics calculations will be performed to gain insight into Coulomb energy and conformations, which can affect dissociation. The impact of internal energy on fragmentation will be assessed by varying the parent ion excitation energy in the FT-ICR and, in the TOF, by augmenting PSD with collisions occurring after ions leave the source. Negative ion dissociation will be compared to that of the corresponding positive ions. In addition, structural factors that influence negative ion production will be investigated. To enhance deprotonated ion yields by MALDI, basic matrices will be developed for peptides.

The Chemistry Department at the University of Alabama Tuscaloosa will acquire a liquid chromatograph mass spectrometer (LC-MS) with this award from the Chemistry Research Instrumentation and Facilities: Multi User (CRIF:MU) program. The requested LC-MS will facilitate ongoing research projects including: cofactor identification and proteomic analysis of photosynthetic systems; elucidation of the role of chromium in human metabolism and its implications in insulin sensitivity and treatments of diabetes; the development of water-soluble ligands for aqueous-phase catalysis and studies of metal-catalyzed modification of nucleosides; preparation and characterization of pentafluorosulfanyl-benzenes and fluorinated polymers for use in a range of industrial applications; and fundamental and applied studies into the sequencing of metallopeptides and deprotonated peptides.

Mass spectroscopy is a basic tool used by physical and biological scientists to identify and characterize materials and chemical species by accurate measurement of their mass as they are vaporized and fragmented in the instrument. Liquid chromatography is a purification technique that separates a complex mixture into individual components before introduced to the mass spectrometer. These are important tools to be used in the training of young scientists. Over 60 student researchers will use LC-MS in their research projects over the next few years. This includes graduate students, undergraduate academic year and summer students (including students from UA's NSF REU program), and high school teachers participating in summer programs. Through the use of an autosampler and cyber-control, educators and researchers located at 4 or more regional undergraduate institutions including two minority serving institutions, will have access to the instrument for the purposes of laboratory classes and undergraduate research.

This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).

The Analytical and Surface Chemistry Program in the Division of Chemistry supports work by Professors Carolyn Cassady and David Dixon at the University of Alabama - Tuscaloosa aimed at enhanced understanding of the gas-phase chemistry of deprotonated amino acid amides and peptides, in order ultimately to provide new approaches to mass spectrometric structure elucidation supporting proteomics and related studies. Combined experimental and computational efforts will provide insight into fragmentation and thermodynamic properties.

The work exposes a diverse group of both graduate and undergraduate students to important interdisciplinary research areas, providing them with tools that will prepare them to contribute to a wide range of chemical biology challenges. Both PIs have also been actively engaged in outreach activities, exposing large numbers of students to the powerful computational and analytical tools utilized in their laboratories.

With support from the Chemical Measurement and Imaging Program in the Division of Chemistry, Professor Carolyn Cassady and Professor David Dixon and their groups will study the gas-phase reactive and dissociative chemistry of deprotonated amino acids, their amides, and peptides by mass spectrometry and computational techniques. The primary focus will be on acidic residues that readily deprotonate, such as phosphorylated serine, tyrosine, and threonine, as well as aspartic acid and glutamic acid. An overall goal is to increase the knowledge of deprotonated peptide fragmentation mechanisms, ion structures, and acid/base properties so that proteomics researchers seeking to sequence peptides by negative ion mass spectrometry will have a strong foundation of fundamental information upon which to base their work. This research will further the development of new methods of analysis of peptides using negative ion mode tandem mass spectrometry, with particular emphasis being placed on electron-based dissociation techniques for sequencing acidic peptides.

This project exposes a diverse group of both graduate and undergraduate students to important interdisciplinary research areas, providing them with tools that will prepare them to contribute to a wide range of proteomic and chemical biology challenges. Both groups are also been actively engaged in outreach activities, such as the University of Alabama Computer Based Honors Program and the Alabama Advanced Instrumental Techniques Colloquium, which expose large numbers of students to the powerful computational and analytical tools utilized in their laboratories.

DESCRIPTION (provided by applicant): The amino acid sequences of peptides affect their biological activity and, consequently, their utility in the diagnosis and treatment of human health issues. The overall objective of this research is to develop procedures for analyzing and sequencing acidic and neutral peptides by mass spectrometry (MS) using electron-induced dissociation techniques. The focus will be on peptides that are difficult to sequence by current mass spectrometry procedures. The first specific aim involves the use of trivalent metal salts to enhance the protonation of peptides by electrospray ionization (ESI). This will result in doubly protonated ions for peptides that normally only singly protonate. This important because the most common electron-induced fragmentation processes, electron transfer dissociation (ETD) and electron capture dissociation (ECD), require that the precursor ion be a multiply charged cation. Trivalent salts of chromium, Cr(III), have been shown to add a second proton to small peptides that normally singly protonate because they contain only one basic site. Other trivalent metals, such as Fe(III), Rh(III), Al(III), and Eu(III), will also be studied to determine if they enhance protonation for small peptides. The mechanism of this effect with is probed. The salt that produces optimum protonation will be evaluated with mixtures of peptides to determine if peptide ion suppression occurs and also to investigate the impact of the salt on chromatographic separations. The second specific aim is to explore ETD and ECD fragmentation pathways that result from multiply protonated peptide ions generated with trivalent metal ions. The development of a trivalent metal reagent should allow analysis of peptide types that has never been studied before by ETD or ECD; for example, it will now be possible to study acidic peptides and neutral peptides with alkyl side chains. Dissociation mechanisms and fragment ion structures with be probed using multi-stage mass spectrometry, including combinations involving collision-induced dissociation (CID) as a second stage. In addition to enhancing protonation, ESI on mixtures of metal salts and peptides often results in formation of metal-cationized peptide ions. For trivalent metals, these complex ions may have added or removed protons from the peptide, resulting in complexes with charges of 2+, 3+, or 4+. The ability of these complexes to undergo ETD or ECD and yield sequence information for a variety of acidic and neutral peptides will be explored. The lanthanide series of trivalent ions wil be studied in detail. The third member of the series, praseodymium (Pr) with atomic number 59, appears particularly suitable for peptide sequencing. Factors to consider in characterizing the use of trivalent metal ion complexes to sequence peptides include metal electron configuration and ionic radius, the location of the metal ion and the extent of protonation or deprotonation in the precursor and product ions, and the types, number, and locations of amino acid residues in the peptide sequence. Density functional theory (DFT) calculations will be employed to gain insight into the structures and energetics involved in these processes.

The Chemical Measurement and Imaging program of the Division of Chemistry supports the research of Professors Carolyn Cassady, David Dixon, and John Vincent from the University of Alabama. Their project improves the sensitivity of mass spectrometry (MS), which is a common analytical tool for identifying and characterizing chemical substances. The researchers use experimental and computational approaches to optimize MS conditions. This project specifically improves MS analysis of peptides. Peptides are used in the study of protein structure and function. The ability to better identify and characterize peptides has benefits for basic molecular biology research, drug development, human health, and biotechnology. Students working on this project receive mentoring and training in an interdisciplinary, collaborative research environment.

This research project improves the sensitivity of mass spectrometry (MS), an important means of characterizing biomolecules. Specifically, the researchers are probing the use of trivalent chromium, Cr(III), to enhance the intensity of the protonated ion signal obtained during the analysis of peptides and other organic molecules. This work includes optimization of experimental MS parameters and determination of the most suitable reagents for inducing proton transfer. Both metal salts and organometallic complexes are studied. The fundamental mechanism of the enhanced protonation process is also being explored. High level electronic structure calculations are used to elucidate the enhanced protonation mechanism with Cr(III) and to determine the locations of the added protons on the organic molecule. This novel Cr(III) method benefits proteomic researchers who use MS to identify peptides in protein digests. The ability to better identify and characterize peptides increases our understanding of biological processes and leads to the development of new pharmaceutical drugs to target specific metabolic pathways.

This award is supported by the Major Research Instrumentation (MRI) and the Chemistry Research Instrumentation Programs. Professor Carolyn Cassady from University of Alabama Tuscaloosa and colleagues Yuping Bao, Jason Bara, Marco Bonizzoni and Paul Rupar are acquiring a matrix assisted laser desorption/ionization time-of-flight mass spectrometer with collision induced dissociation (CID) capabilities (MALDI/TOF-TOF MS.) In general, mass spectrometry (MS) is one of the key analytical methods used to identify and characterize small quantities of chemical species in complex samples. MALDI TOF combines gentle ionization (ideal for producing intact ions of peptides, proteins, nucleic acids, carbohydrates, synthetic polymers, and other similarly sized species) with a detection mode that offers an excellent balance between sensitivity and accuracy across a wide mass range. This highly sensitive technique allows identification and determination of the structure of molecules in a complex mixture. The acquisition strengthens the research infrastructure at the university and regional area. The instrument broadens participation by involving diverse students with this modern analytical technique. It is also used in outreach activities, such as the annual Alabama Advanced Instrumental Techniques Colloquium (AITC), which exposes undergraduate students from throughout the region to state-of-the-art instrumentation. Students in an NSF Research experiences for Undergraduates (REU) program in chemistry and materials science also use the MALDI/TOF-TOF MS.

This mass spectrometer enhances research and education at all levels. It aids researchers in developing techniques for the analysis and sequencing of acidic peptides using deprotonated ions and for characterizing structures, molecular weights and other properties of polymer-ionene hybrids. The MALDI/TOF-TOF MS is used to examine iron oxide nanoparticle platforms for a variety of biomolecules and polymers. The instrumentation is also used for characterizing host-guest complexes of hyperbranched polyelectrolytes and analyzing polyimines produced by anionic ring opening polymerizations.