Vicki H. Wysocki - US grants

There is no question that determination of the primary sequence of peptides and proteins is important to our understanding of living systems. The proposed research will address several different questions involving singly and multiply protonated peptides. All of the related projects are designed to increase the current understanding of the hydrogen bonding interactions and fragmentation patterns of activated protonated peptides. The long range goals of this work are to provide additional "rules" that can be used to enhance automated primary sequencing of peptides and proteins by tandem mass spectrometry and, ultimately, to relate information on gas-phase fragmentation patterns and energetics of dissociation to peptide and protein conformation. In the proposed research, internally cold protonated peptides will be formed by electrospray ionization. Mass-selected ions will be activated by collisions with a surface over a range of collision energies. The experiments will probe, as a function of amino acid sequence, (i) the influence of hydrogen bonding on molecular conformation and stability and (ii) the mobility of protons in molecules with different internal energy contents. The detailed data on energetics of dissociation will be used to determine mechanisms of fragmentation and the sequence, size, and charge state dependence of the peptide fragmentation efficiency curves. The mechanistic implications of these results will then be sought. The experimental work will be supported by quantum chemical calculations, including determinations of bond orders and energy partitioning values (diatomic energy contributions), which will be used to predict fragmentation pathways. Insight into the excitation mechanism of SID and into the fundamental aspects of fragmentation of large molecules will also be gained. If the relative energetics of fragmentation efficiency vary significantly with peptide sequence (see preliminary results), a concrete link between energetics of gas phase fragmentation and sequence-specific molecular stabilization will be established.

This award from the Academic Research Infrastructure (ARI) Program will assist the Department of Chemistry at the University of Arizona acquire a hybrid mass spectrometer (MS) with an electric sector (E)-magnetic sector(B)/curved field reflection time-of-flight (TOF) geometry. This equipment will enhance research in a number of areas including the following: (1) design and synthesis of a variety of biologically active linear and cyclic peptides, pseudopeptides, peptidomimetics and complex peptide libraries (2) structure/physical property/reactivity relationships in hemes and heme proteins (3) studies of the enzyme and compounds that mimic features of the molybdenum and heme centers of the enzyme (4) synthesis and characterization of new organic compounds (5) synthesis of carbohydrate based natural product analogs and the development of novel carbohydrate based materials (6) design and synthesis of novel amphiphilic molecules that form organized assemblies upon solvation (7) novel organic snthesis methodology to synthesis of novel materials, and (8) mechanism of lipid transport in insects. Mass spectrometry (MS) is a technique used to probe intimate structural details and to obtain the molecular compositions of a vast array of organic, bioorganic, and organometallic molecules. The addition of the technique of electrospray extends the range of MS to proteins and nucleic acid molecular weights far beyond any other technique. The use of electrospray ionization in combination with high resolution provides the latest techniques available in mass spectrometry. It affords the chemist one of the most powerful tools available for the characterization of compounds. The acquisition of this capability in mass spectrometry is essential for the prosecution of frontier research in many fields of chemistry.

The long-term goal of the research proposed here is to improve the throughput and accuracy of automated tandem mass spectrometric peptide and protein sequencing. There are three specific aims in the proposal: (1) Continue investigations of enhanced cleavage at acidic amino acidic residues in order to confirm structural features that lead to enhanced cleavage. Use ion mobility (ion chromatography) spectrometry and molecular modeling to confirm whether proposed secondary structure leads to unusual fragmentation. (2) Use the SEQUEST program and known proteins to search for structural features that cause unusual fragmentation patterns. SEQUEST is a program that is generally used to correlate uninterpreted product ion MS/MS spectra with sequences from protein and nucleotide databases. In our study, the SEQUEST program will be used as a tool to identify sequence stretches that give spectra that are not correctly predicted based on the current state of knowledge of peptide dissociation. Perform detailed mechanistic studies to clarify/identify the structural features leading to the unusual fragmentation patterns and develop "rules" that can be made available for incorporation into automated sequencing protocols. (3) Compare the gas-phase collision- induced dissociation and surface-induced dissociation activation methods to determine whether surface-induced dissociation provides a quantifiable improvement in sequence determination by tandem mass spectrometry. Determine whether sequence identification can be obtained by surface-induced dissociation of small proteins without prior digestion, using chemokines as representative structures. These different, but related, projects are expected to increase our fundamental knowledge of peptide dissociation in the gas phase, improve practical automated sequencing of peptides, and characterize whether the surface-induced dissociation activation method should be pursued as a versatile method for practical sequencing of peptides and proteins.

This proposal requests a high performance, high throughput MALDI-TOF-MS, a mass spectrometer (MS) that couples matrix-assisted laser desorption/ionization (MALDI) with a time-of-flight (TOF) applications for the instrumentation are (1) Victor J. Hruby, Glucagon Structure- Function Studies; New Modalities for Treatment of Pain and Drug Abuse; Peptide Hormone Structure and Function; Opioid Receptor-Specific Peptides; (2) F. Ann Walker, Structure/Physical Property/Reactivity Relationships in Heme Proteins (Cytochrome Models, Nitrophorins, Arsine Binding to Hemoglobin); (3) John H. Enemark, Structural Models for Molybdoenzymes; (4) Vicki H. Wysocki Surface-induced Dissociation; (5) Jaqueline Gervay, Characterization Studies of the in situ Equilibria Occurring in Colominic Acid Oligomers Targeted for Delivery to the HIV Cell Surface Glycoprotein, gp120, and (6) David F. O'Brien, Selective Polymerization of Specially Designed Reactive Lipids. The access to state-of-the-art, high throughput mass spectrometer to analyze samples not amenable to characterization with the current facility instrument is critical to the maximum productivity and success of these projects. The University, the College of Science, and the Chemistry Department have made a strong commitment to the project by providing recently renovated space for an improved mass spectrometry facility, by staffing the facility with two full time mass spectrometry specialists (Ph.D. and M.S. level) and two graduate student RA positions, and by providing cost sharing in the amount of $75,000.

This project, carried out by Professor Vicki H. Wysocki and her students at the University of Arizona and supported by the Analytical and Surface Chemistry program, develops a novel surface characterization tool to provide qualitative identification and quantification of the functional groups present in the outermost atomic layers of organic thin films. The core of the method is use of hyperthermal collisions of atomic and polyatomic ions with these surfaces, and subsequent study of ion/surface reactions, neutralization yields, projectile dissociation efficiency, and chemical sputtering to determine the surface composition. Hyperthermal collisions are used to study single composition and mixed composition model surfaces, many of which are composed of thiolate self-assembled monolayers and Langmuir-Blodgett films. Contact angle, FTIR, atomic force microscopy, ellipsometry, and XPS measurements are also used as independent analytical probes of the surface composition.

Professor Wysocki and her students at the University of Arizona use the carefully controlled collisions of slow moving ions with surfaces to reveal the composition of the organic overlayers on those surface. Subtle features of the surface are revealed by using more complex structures for the incoming ions. Chemical reactions between the surface and the incoming ions are also used to reveal structure and composition. The slowness of the incoming ion means that only the top few atomic layers of the surface are examined. Reactivity and structure of such thin films is of major interest area in areas such as sensors, catalysis, and new electronic devices.

0140644
Wysocki
This award provided support for a workshop entitled "Analytical Instrumentation for the New Millennium - Biological Sciences" to be held Dec 2-5, 2001 in Tucson, Arizona. The workshop will bring together scientists with broad interests in biological measurements, including both the biologists who need the measurements and the instrument developers who design and build instrumentation. The format of the workshop will include highlight presentations by cutting-edge researchers who will conclude with a brief description of goals for the future and the major obstacles to be faced in meeting those goals. These presentations will be followed by breakout sessions to critique/evaluate the proposed goals and obstacles. The expected outcomes of the workshop are a report to be written jointly by the breakout leaders and organizers and presentations to be made at national meetings. This workshop is jointly supported by the Directorate for Biological Sciences and the Directorate for Mathematical and Physical Sciences.

A grant has been awarded to Dr. Vicki Wysocki at the University of Arizona to
design and construct an improved quadrupole-time-of-flight (Q-TOF) tandem mass spectrometer (MS-MS) designed to include two complementary activation methods, surface-induced dissociation (SID; surface target) and collision-induced dissociation (CID; gaseous target). Two biological measurement challenges that will be addressed by the proposed instrument are (1) protein identification from complex mixtures with improvements in numbers of total correct identifications and (2) analysis of glycoconjugates, specifically glycosphingolipids, from complex mixtures without prior deglycosylation. The proposed instrument will consist of the following components: a combination ion source (atmospheric MALDI and micro/nanoESI); a quadrupole mass analyzer to select ions of interest for activation; a surface for surface-induced dissociation; a hexapole for collision-induced dissociation or for trapping of surface-activated ions; and an orthogonal TOF chamber for analysis of product ions produced by CID or SID. This project will result in an instrument with several enhanced capabilities and in an excellent training experience for project members. The instrument will provide high sensitivity, flexibility in ion activation, a high duty cycle, high resolution and high mass accuracy for product ions, and fast acquisition of spectra (compatible with microcapillary LC introduction into the ESI source). Successful development of this instrument will have a significant impact on proteomics research.

DESCRIPTION (provided by applicant): This proposal requests a Thermo Finnigan ProteomeX DECAP-51000 Integrated Workstation, an ion trap mass spectrometer equipped with LC pumps, a 10 port switching valve, strong cation and reversed phase columns for multidimensional chromatography, and a nanospray probe. This instrument will serve the needs of a number of University of Arizona bioscience researchers. The major users and their applications for the instrumentation are (1) Samuel Ward, Molecular and Cellular Biology, Study of signaling pathways during cell differentiation in the Nematode C.elegans, genes are homologeous to human disease genes linked to Alzheimer's and muscular dystrophy; (2) Brian Larkins, Plant Sciences, College of Agriculture and Life Sciences, Identificationand Analysis of Proteins Required for Improved Maize Protein Nutritional Quality; (3) M. Halonen/D. Vercelli/F. Martinez/M. Cusanovich, Center for Respiratory Sciences, Transcription Factors that Bind Regulatory Elements in the Immunoglobulin G4 Germline Promoter, the IL-13 Promoter, and the CD 14 Promoter; Cellular and Molecular Mechanisms of Asthma (4) Elizabeth Vierling, Molecular and Cellular Biology, Molecular chaperone function; expression and function of cytoplasmic organelle and heat shock proteins, the pathways studied are critical to normal cell function; (5) Carol Dieckmann, Biochemistry, Identification of Mutations in Genes Coding for Major Polypeptides in the Chlamydomonas Eyespot;, (6) Thomas Baldwin, Biochemistry, Pulsed Alkylation MS to Investigate Protein Folding in Bacterial Luciferase; (7) Vicki Wysocki, Chemistry, Mechanisms and Energetics of Peptide Dissociation, this work is directly applicable to the identification of proteins from biological organisms. Modern protein research cannot be accomplished without mass spectrometry. The access to a dedicated microflow LC-mass spectrometer with a nanospray probe to characterize samples that are not amenable to analysis with the current mass spectrometry facility instruments is critical to the maximum productivity and success of these projects. The University has made a strong commitment to the project by by renovating space for a new "branch" mass spectrometry laboratory that is located in Biosciences, by hiring a full time Ph.D. biological mass spectrometry specialist (about $60,000 per year), by providing funds for a Director of Proteomics (about $80,000/year) and a technician (about $35,000/year) to help with sample preparation, and by providing cost sharing in the amount of $75,000.

Professor Vicki Wysocki of the University of Arizona is supported by the Analytical and Surface Chemistry Program to study the fast fragmentation of peptides. The fundamental question in this work is one that asks why we are able to see significant fragmentation on the timescale of the typical mass spectrometry experiment, while the best theory available suggests that fragments should only be observed with longer timescale MS experiments. The overall hypothesis is that there are fast fragmentation pathways (via previously undescribed reactive intermediates) that lead to the appearance of products on timescales that allow observation by mass spectrometers with microsecond or shorter experimental timeframes. The PI uses surface collisions in combination with matrix-assisted laser desorption ionization (and later electrospray ionization) and time-of-flight mass spectrometry to probe these processes. The question is studied by varying both the nature of the surface and the nature of the projectiles. There is a well-established collaboration with the Futrell group at PNNL and the theorist Hase at Texas Tech. Students are well-trained in physical-analytical chemistry and mass spectrometry.

Fragmentation of peptides is commonly used in proteomics, in which mass spectrometry plays a critical role. Understanding fragmentation at a fundamental level can lead to more efficient analytical instruments, and predictive models for database purposes.

Proteins play a central role in living organisms, serving, for example, as enzymes that catalyze metabolic reactions, as structural or mechanical units, and as cell signaling molecules. The field of proteomics, which entails large scale identification and structural characterization of proteins, depends strongly on tandem mass spectrometry (MS/MS) and database searches that make use of MS/MS spectra. The overarching goal of this proposal is to improve automated peptide and protein identification by tandem mass spectrometry. The proposed research will identify and comprehensively characterize clusters of fragmentation behavior for peptides activated by two major complementary MS/MS activation methods, electron transfer dissociation (ETD) and collisionally- activated dissociation (CAD), when both are applied in two prominent instrument platforms used for proteomics experiments (linear ion trap and quadrupole time-of-flight, QTOF). The underlying hypothesis guiding this research is that the computer algorithms that are used for peptide and protein sequencing, identification, and quantitation, and the embedded data acquisition software, can be improved by statistically analyzing how peptides fragment at a molecular level. A priori knowledge of the behavior of differenct amino acids provides significant insight into the possible fragmentation patterns observed and the MS/MS spectra and these data will be used to improve data acquisition and data analysis. This research brings together three research groups, the Wysocki group with expertise in peptide fragmentation mechanisms and data mining, the Tseng group with expertise in biostatistics/ bioinformatics( to perform clustering plus classification and regression tree analysis of large spectral datasets), and the Coon group, developers of electron transfer dissociation (ETD) in the linear ion trap/Orbitrap mass spectrometer.

[unreadable] DESCRIPTION (provided by applicant): [unreadable] The University of Arizona proposes to acquire a ThermoFinnigan LTQ-FT high performance mass spectrometer (MS). This instrument will be placed in the UA Mass Spectrometry Facility and operated by staff of the MS facility and the proteomics facilities. This instrument's main attractive features are that it combines linear ion trap (LTQ) high throughput performance on an HPLC timescale with ion cyclotron resonance (FTMS) high resolution and high mass accuracy. FTMS resolution of 100,000-500,000 provides mass accuracy of 1-2 ppm, and the LTQ provides sensitivity in the sub-fmol range. Fragmentation by collision-induced dissociation and electron capture dissociation are possible and provide complementary fragmentation information. Infrared multiphoton dissociation can provide information similar to CID, but with the possibility of activating fragment ions as well as precursor ions and can be used to pre-heat ions for ECD. A major user group that already uses mass spectrometry to solve biological or medical problems, but who have faced limitations in their research because they do not have access to a higher performance instrument such as the LTQ-FT, has been identified. These include faculty from Biochemistry and Molecular Biophysics (Vierling, Little), Pharmacology and Toxicology (Lau, Monks, and Vaillancourt), the Arizona Cancer Center (Gerner), Chemistry (Wysocki), and the Valley Fever Center for Excellence, VA Hospital (Galgiani). The types of problems that will be solved for these investigators with the proposed LTQ-FT MS are grouped into (1) those involving detailed structural studies of specific proteins and protein complexes, (2) identification of post-translational modifications, and (3) structural characterization problems not involving proteins (drugs, prostaglandins) [unreadable] [unreadable] [unreadable] [unreadable]

0722579
Chorover
This MRI proposal requests funding for two tandem mass spectrometers with a research focus on water quality and its biogeochemical and anthropogenic controls. Emphasis is placed on emerging contaminants and their carriers, since these constituents are impacting to an increasing degree all aspects of the hydrologic cycle and they pose some of the most complex and broadly relevant challenges for water science and engineering. Faculty in four colleges at University of Arizona (UA), along with collaborators at Arizona State University (ASU) and Northern Arizona University (NAU), are establishing a new multi-user facility dedicated to state-of-the-art water analyses that will provide a keystone for current and future programmatic needs in this cross-cutting area of environmental science, engineering and toxicology. The MRI will be included in this new facility, and will be used by more than 18 engineering and science faculty collaborators with research and teaching programs focusing on groundwater, surface water, drinking water and wastewater. All share the common goal to characterize and quantify dissolved and suspended species in aqueous systems. The MRI request is for (i) liquid chromatography tandem mass spectrometry (LC-MS/MS) and (ii) gas chromatography tandem mass spectrometry (GC-MS/MS).

Chemistry (12). This project is building on the National Research Council's "Beyond the Molecular Frontier" to create a matrix based on four "ways of thinking" and four central, compelling questions that are then used to construct an innovative general chemistry curriculum for science and engineering majors. This curriculum is shifting the focus from learning a body of knowledge to understanding chemistry as a way of thinking. The learner-centered classroom and laboratory curriculum is also building on existing, exemplary materials developed by the NSF chemistry initiatives. Assessment tools embedded in the curriculum are being combined with a comprehensive evaluation plan that includes qualitative and quantitative measures. The combination of research university faculty and community college faculty from two campuses is allowing testing of the curricular materials among three diverse populations including substantial numbers of Hispanic and Native Americans students, contributing to the quality of the curriculum, and the broader impact of the project.

The PSWRCE Protein and PCR MS Core will collaborate on the following projects: Specific Aim i - Proteomics Analyses for Burkholderia, Coccidioides, and Reservoir Vaccines Projects [unreadable] Identify protein biomarkers for use as diagnostic or vaccine candidates (from serum, urine, and lung homogenates, with depletion of abundant mouse/human proteins as necessary) [unreadable] Perform comparative proteomics on pre-fractionated samples (e.g., extracellular proteins or cell wall proteins of two different strains of an organism, or wild type vs. mutant) [unreadable] Build "blood meal" protein library to use to identify host vertebrate proteins in tick nymphs Specific Aim 2 - Development of Diagnostic Assays [unreadable] Use biomarker IDs of Sp. Aim i to develop bioaffinity MS for pathogen identification [unreadable] Use MS to guide development of targeted ELISA or other fluorescence assays (characterize expressed protein antigens, antibodies, and labeled antibodies by MS throughout development of assay) [unreadable] Compare antibodies vs. small ligands for capture of antigens in bioaffinity MS Specific Aim 3 - Ibis TSOOO PCR-MS Biosensor Applied to Reservoir Vaccines, Burkholderia &Coccidioides [unreadable] PCR MS (on mitochondrial DNA) for ID of vertebrate host on which vector has fed (e.g., tick nymph fed on mule deer) and ID of tick-borne pathogenic organism present [unreadable] PCR MS for rapid ID and strain typing of pathogens, as well as confirmation of the presence of toxin genes, antibiotic resistance genes, selected virulence factor genes Specific Aim 4 - Characterization of Protein Complexes (uncompensated synergistic activity) [unreadable] Structurally characterize large protein-protein complexes (e.g., pili involved in virulence, assemblies of bacteriophage tail fiber proteins useful for biosensors) using a one-of-a-kind modified QTOF MS The antigen discovery coupled to support of diagnostic assay development, PCR-MS, bioaffinity MS, and structural characterization of large protein-protein complexes are unique capabilities of the core.

Support from the National Science Foundation Major Research Instrumentation Program has allowed work to begin on a project to design and produce an innovative ion mobility surface-induced dissociation mass spectrometer that can produce much more structural information on large non-covalent protein complexes or other macromolecular assemblies than is possible with present commercial instrumentation. Proteins often carry out their functions by working together in non-covalent multi-protein complexes. Characterization of the composition, numbers, conformations, and spatial arrangements of the subunits in a protein complex is challenging because of the total complex size, the presence of a biological matrix, and the fragile nature of the non-covalent bonding of the subunits to each other. We propose to design an ion mobility/surface-induced dissociation mass spectrometer that can measure the m/z and shapes (collision cross sections) of large non-covalent protein complexes and effectively fragment shape-selected complexes to characterize the composition and structure of the complex. The development project will improve the infrastructure for structural biology research by providing a nanoelectrospray/ion mobility/surface-induced dissociation tandem mass spectrometer that can characterize non-covalent protein complexes at a level not possible with current instrumentation. The scope of potential use of the proposed instrument is broad: biological problems that will be addressed will focus on determination of the stoichiometry and spatial arrangement of sub-units in non-covalent proteinprotein and protein-ligand complexes. The development project itself will be an excellent vehicle for combining research and education, producing students and postdoctoral associates who will learn how to work in teams and who will be cross-trained in the purification, handling, and analysis of biological macromolecular complexes and in instrument development. The research results will be presented in the peer-reviewed literature, at local seminars, to industrial collaborators, at national and international conferences, in graduate lectures by the PI at UA in Chemistry and Biochemistry courses, and in the MS/MS short course taught by the PI and colleagues each year at the annual national meeting of the American Society for Mass Spectrometry. The PI's research group will also work with two local 6th grade science teachers at Mansfeld Middle School in Tucson - a school where the majority of students are Hispanic (68%).

DESCRIPTION (provided by applicant): The Ohio State University proposes to acquire a Bruker solariX 15 tesla Fourier Transform Ion Cyclotron Resonance mass spectrometer (FTICR MS). This versatile high-end instrument will be placed in the OSU Mass Spectrometry and Proteomics Facility (MS&P) within the Campus Chemical Instrument Center (CCIC), a campus-wide Center that is administratively housed in the OSU Office of Research. The instrument will be operated by staff of the MS and proteomics facility and selected highly trained personnel from mass spectrometry and major user research groups. This instrument's main attractive features are its breadth of application, with a dual MALDI and ESI source coupled to ultrahigh resolution and high mass accuracy. The proposed FTICR MS provides resolution of up to 40,000,000, sub ppm mass accuracy, and sensitivity down to the 100 amol range. Fragmentation by collision-induced dissociation and electron transfer dissociation (ETD), in the external collision cell, and sustained off-resonance irradiation (SORI) and electron transfer dissociation in the ICR cell are possible and provide complementary fragmentation information. CASI (Continuous Accumulation of Selected Ions) is available to enrich very low abundant species by trapping in the collision cell, even from tissue imaging. A major user group that already uses mass spectrometry to solve biomedical problems, but that have faced limitations in their research because they do not have access to a higher performance instrument such as the solariX, has been identified. These include faculty from the College of Medicine (Torrelles, Rovin, Freitas, Parthun), the Comprehensive Cancer Center (Clinton), Chemistry and Biochemistry (Bruschweiler, Foster, Musier-Forsyth, and Turro), and Physics (Poirier and Zhong). The types of problems that will be solved for these investigators, and techniques that they will use with the proposed solariX FTICR MS, include (1) high resolution MALDI and MALDI imaging of tissue, (2) detailed high end, top down structural studies of specific histone proteins and post-translationally-modified proteins, (3) native mass spectrometry measurements to gain stoichiometry and topology of protein complexes, and (4) complex mixture analysis for structural characterization of metabolites and metal-DNA complexes. The CCIC MS&P Facility is an established, well utilized university-wide core. It provides an optimum environment for a high end instrument - a vigorous research community with great need for such an instrument and OSU faculty and staff with the enthusiasm and expertise to use the solariX to its greatest potential. If funded, the solariX will be invaluable to a very broad constituency of researchers.

An award is made to Ohio State University to develop and instrument that can characterize protein complexes through improved dissociation of the complexes in mass spectrometers. Proteins in living systems can play structural roles, such as those in skin and hair; they can also play active roles such as enzymes that help with digestion, or hemoglobin that carries oxygen and carbon dioxide through the body. Cellular processes such as metabolism, cell signaling, gene expression, trafficking, cell cycle regulation, and the formation of subcellular structures are contingent upon the formation and dynamic interactions of complexes/assemblies of proteins. These protein complexes may also be bound to other biomolecules (DNA/RNA), interacting in specific ways. Because protein structure is tied to function, effective tools are needed to characterize protein-protein and protein-ligand complexes. The proposed research will result in integration of surface-induced dissociation devices into multiple types of mass spectrometers that will provide information on the structures of protein complexes important in biology. Discoveries from the project will be presented in university courses and at international, national, regional, and local workshops/ conferences on mass spectrometry and biomolecule structure and in the peer-reviewed literature. The undergraduate and graduate students and the postdoctoral associate will be trained in instrument development and will also gain collaboration skills through interactions with the private sector partners and local electronics and machine shops. Early SID adopters will serve as a direct sounding board for the success of modifications. The project is vendor- and platform-neutral, with direct inclusion of multiple private sector partners, Ardara Technologies, Waters (Q-IM-TOF, quadrupole ion mobility time of flight), Thermo (Orbitrap), and Bruker (ICR, ion cyclotron resonance), providing the project team an opportunity to present at company user meetings and an opportunity for those partners to assess the commercial value of the instrument modification.

This research will develop surface-induced dissociation (SID) in high/ultra-high resolution mass spectrometers and refine its use in an ion mobility (IM) mass spectrometer whose purpose is to characterize protein complexes. The proposed research will benefit researchers from many different fields interested in the characterization of the topology of protein complexes. Planned, collaborative visits to Thermo and Bruker are a necessary part of the research, to gain familiarity with needed instrument platforms, to plan modifications, and to allow the vendors to assess progress. The final instrument configurations will combine either IM or high/ultrahigh resolving power with efficient SID fragmentation and enhanced collection of product ions. The proposed combinations are currently unavailable on any commercial instrument and are expected to enhance the quality of analysis and expand the range of biological samples that can be effectively characterized by mass spectrometry (MS). Planned improvements to SID utilize RF focusing of the ions departing the surface post collision, in contrast with the DC-only focusing that has been used in the past. Inclusion of SID in current commercial ultra-high resolution platforms has not yet been accomplished and is expected to dramatically enhance both the scope and depth of analysis on biological systems. In the Bruker instrument, the modification will allow SID to be explored, not only as a possible additional activation method, but as a replacement for collision-induced dissociation (CID). The overall intellectual merit of the project is adaptation of high performance mass spectrometers to include a higher performance activation method for fragmentation of refractory analytes, for which existing methods fail to provide direct substructure information.

? DESCRIPTION (provided by applicant): Salmonella enterica serovar Typhimurium (Salmonella) is one of the most significant food-borne pathogens affecting humans and agriculture. It has long been thought that nutrient utilization systems of Salmonella would not make effective drug targets because there are simply too many nutrients available to Salmonella in the intestine. However, we have discovered that during growth in the inflamed intestine Salmonella relies heavily on a single nutrient - fructose-asparagine (F-Asn), which is present at high concentrations in human foods. Mutants that cannot acquire F-Asn are severely attenuated suggesting that F-Asn is the primary nutrient utilized by Salmonella during inflammation. No other organism has been reported to synthesize or utilize this compound, although we suspect that a few other pathogens and members of the normal gut microbiota can utilize it. The apparent lack of F-Asn utilization pathways in mammals and most other bacteria suggests a specific and potent therapeutic target for Salmonella. The locus encoding F-Asn utilization, fra, provides an advantage only if Salmonella can initiate inflammation and use tetrathionate as a terminal electron acceptor for anaerobic respiration (the fra phenotype is lost in Salmonella SPI1- SPI2- or ttrA mutants, respectively). We hypothesize that if Salmonella can initiate inflammation (or enters a gut that is already slightly inflamed), it can begin tetrathionae respiration during F-Asn catabolism and thereby outcompete the normal microbiota, which are doubly compromised by the inflammation and their ability to only ferment (but not respire) F-Asn. We will test this central postulate and build the foundation for two types of therapeutics to block Salmonella acquisition of F-Asn. In our first specific aim, we will investigate the role of a asparaginase (FraE), kinase (FraD) and deglycase (FraB) in F-Asn utilization. Through biochemical characterization of the individual reactions catalyzed by these Fra enzymes and development of high-throughput assays, we expect to facilitate future screens that will identify small molecule inhibitors of these enzymes. We hypothesize that the FraR transcription factor is a repressor. Therefore, preventing its release from the fra operon promoter would also be of therapeutic interest. We propose to determine the natural inducer of FraR and determine the DNA binding sites of FraR in the fra operon. In the second aim, we plan to employ a combination of metagenomics, selective growth in the presence of F-Asn, and bioinformatics to test the idea that in healthy gut communities there are select members of the microbiota that utilize F-Asn and prevent Salmonella from acquiring this nutrient. Finally, we expect our findings on the enzymology and regulation of F-Asn utilization in Salmonella, and possible competing intestinal microbes, to inform our efforts to design new probiotic bacteria that can reduce the severity and duration of Salmonella infection in mice. Overall, our efforts will lead to a better understanding of Salmonella growth in the inflamed intestine and to novel therapeutics.

? DESCRIPTION (provided by applicant): Characterization of the overall topology and inter-subunit contacts of protein complexes, and their assembly/disassembly and unfolding pathways, is critical because these complexes regulate key biological processes, including processes where malfunction leads to disease. Although many protein complexes can be characterized by existing tools, including X-ray crystallography and NMR, others are not amenable to these approaches. One solution to this gap in the field is addition of native mass spectrometry (MS) tools to the suite of structural biology approaches. While native MS has provided many useful insights on protein complexes, the most common activation method, collision-induced dissociation (CID, multiple low-energy collisions with gaseous targets to induce fragmentation), often induces an unfolding pathway that produces highly charged unfolded monomers and complementary (n-1)-mers,. This information is insufficient to directly characterize the topology and intersubunit contacts of the complexes. Surface-induced dissociation (SID), in contrast, has been shown by the PI's lab to induce direct dissociation to subcomplexes and to also effectively probe subtle structural changes that are not evident from CID spectra (e.g. pre-unfolding in the ion source). The overarching goal of this proposal is to develop this novel, alternative MS activation method, surface-induced dissociation coupled to ion mobility (SID/IM), as a tool for characterization of structural features of multimeric protein complexes so that these features can be tied to function. Aim I is to characterize pentraxin-ligand structures of increasingly highe complexity, including binding of metal ions plus small molecular ligands and protein ligands to C-reactive protein and PTX3. Aim II will determine whether SID/IM can define the structural features and unfolding propensity of ROP (repressor of primer) dimer mutants and ROP mutant:RNA complexes. Aim III will determine whether SID/IM can define whether discrete modifications of histone proteins influences nucleosome (histone:DNA) fragmentation/disassembly in ways related to their expected destabilization. Aim IV will utilize SID/IM to characterize a lipid:protein complex (CRP:DMPC), membrane receptor:protein complex (CTB:GM1) and membrane proteins (rhodopsin, aquaporin0, YidC, YidC:Pf3 coat) sprayed from detergent (e.g., DDM), amphipols, or nanodiscs. Multiple collaborators, experts in the production/purification/functional behavior of particular protein complexes but who need access to better characterization tools, have agreed to provide proteins of varying complexity (Bortazzi (Instituto Clinico Humanitas; PTX3); Magliery (OSU; ROP mutants); Poirier and Ottesen (OSU; modified nucleosomes); Brown (UA; rhodopsin); Schey (Vanderbilt; AQP-0); Dalbey (OSU; YidC, Pf3 Coat). Characterization of the innovative SID/IM approach, direct comparison with CID/IM, and development of knowledge of sample types where the SID approach is vital to protein complex structure determination, is critical for the continued development of native MS as a strong structural biology tool.

We propose a Resource for Native Mass Spectrometry Guided Structural Biology that will be led by a team of scientists including experts in MS instrumentation (Wysocki, OSU; Russell, Texas A&M), separation science coupled to ionization (Olesik, OSU; Badu, OSU; Holland; WVU), and computational chemistry (Lindert, OSU). The goal of this Resource is to build and validate an integrated workflow for structural characterization of protein:protein, membrane protein:lipid, and protein:RNA complexes that are critical for an array of cellular and organismal processes. There is a growing appreciation of the pivotal role and utility of MS-based approaches for structural characterization of biomacromolecules, filling critical gaps and complementing other structural biology tools. Thus, our workplan leverages innovative MS methods to determine: (i) m/z of all binding partners and the intact complex, (ii) component stoichiometry, (iii) heterogeneity, if present, (iv) the relative topology/architecture/ conformational diversity of components in the complex, and (v) the hierarchy of assembly, including binding affinities of individual subunits. Investigators from across the United States (in WA, OR, UT, CA, AZ, TX, TN, OH, MD, MA) and international sites will contribute challenging biomedical projects on topics including viral hemorrhagic fevers, HIV, cataract formation, and neurological disorders. Our workflow is designed to advance understanding of: (i) how formation of and dynamic changes in wide- ranging macro-molecular assemblies determine their biological roles, (ii) how alterations in assembly/architecture of these complexes lead to disease, and (iii) foundational principles for building synthetic mimics needed for biomedical applications. In this Resource, ten Driving Biomedical Projects (DBPs) provide biomedical structural characterization challenges and serve as drivers and test beds for five Technology Research and Development (TR&D) projects. The TR&Ds provide: (i) effective separation methods to purify and deliver native macromolecular complexes well suited for MS, (ii) effective surface-induced dissociation and UV-photodissociation technologies, (iii) measurement of the intact complexes and their non-covalent (sub-complex) and covalent dissociation products with high resolution ion mobility (IM) and/or MS, and (iv) computational tools for structure prediction. Computational tools will use restraints from surface-induced dissociation patterns and collision cross sections from IM-MS experiments, and from MS-based solution measurements (H/D exchange and covalent labeling). Existing ties between the TR&Ds and instrument companies (Waters, Thermo, Bruker, Sciex, Phenomenex) as well as a national laboratory (PNNL) will aid technology development and expedite technology dissemination. Our training and dissemination activities (e.g., workshops, beta device installations) are designed to increase outreach and maximize Resource payoffs.

TR&D 1 Project Summary. Surface induced dissociation (SID) has emerged as an effective tool for probing the topology of protein complexes in the field of native mass spectrometry (nMS). SID has the unique advantage of efficiently cleaving the interfaces of noncovalent protein complexes to yield monomer subunits as well as small order oligomers. Additionally, SID products typically retain compact/highly structured conformations such that ion mobility measurements coupled with SID can be used to gain insights into protein subunit structure through collision cross section (CCS) measurements. This TR&D aims to improve SID technology across multiple mass analysis platforms that are used in the nMS field (namely quadrupole-time-of- flight (QTOF), OrbitrapTM, and Fourier transform ion cyclotron resonance (FTICR) platforms). Current SID devices span 3-4 cm of an instrument?s ion path with at least ten DC electrodes. These electrode voltages can be tuned to direct ions toward an off-axis surface (relative to the ion path within an instrument for the activating ion-surface collision and subsequent collection of product ions back onto the original ion trajectory axis. Lenses may also be tuned to guide ions through the device without activation, allowing for standard MS experiments to be conducted (so-called ?flythrough? mode). Aim 1 of this TR&D is to simplify the tuning of SID experiments while retaining or improving ion transmission efficiencies in both SID and ?fly-through? experiments. A new SID device containing an on-axis collision surface and ion carpet will be developed to require fewer electrodes than current SID devices, thereby simplifying tuning requirements for SID. The radial-focusing nature of the ion carpet array is expected to assist ion transmission efficiencies. The device will be implemented in a prototype higher resolution QTOF. Aim 2 will adopt advances made in Aim 1 to improve current SID performance within Orbitrap platforms for high resolution nMS experiments. There is also an SID acceleration voltage limit of roughly 70 V for current Orbitrap configurations. Collaboration with Thermo Fisher will facilitate progress by providing the schematic information necessary to incorporate independent power supplies into electronic boards on the QExactive+ EMR platform at OSU and QExactive HF UHMR platform proposed for purchase. This collaboration will also facilitate adapting technology developed from Aim 1 into the ion optics within Orbitrap Exactive platforms. Aim 3 focuses on improving SID technology in an FTICR platform. Currently, this platform has a maximum quadrupole mass isolation limit of m/z 6000, which is too low for selection of larger protein complexes. There is currently a diminished performance in the collection of collision induced dissociation fragments due to the original collision cell space being split between an SID device and truncated collision cell. Both of these shortcomings will be addressed through instrument redesign in collaboration with the vendor (Bruker) as described in Aim 3.

Project Summary: Administration and Management. The proposed Resource for Native Mass Spectrometry Guided Structural Biology ( ) brings together a team of outstanding scientific nMS?SB Resource leaders who, with the support of select staff, postdoctoral researchers, and graduate students, are well-equipped to collaboratively advance the proposed science, dissemination, and training. This team will work together to produce an integrated workflow for structural characterization of protein:protein, membrane protein:lipid, and RNA:protein complexes. The proposed characterization workflow will lead to a better understanding of how protein complexes carry out their normal biological functions, how alterations in architecture lead to disease, and how to build synthetic mimics to carry out desired biomedical applications. Through integration of all components of the nMS?SB Resource (TR&Ds, DBPs, and Community Engagement), we will steer conversion of the developed native MS workflow from an appealing technology used by specialists and their collaborators to a widespread frontline tool that can be used to guide other biochemical and structural tools. The overall goal of the Administration and Management Core is to ensure that the vision of the Resource for Native Mass Spectrometry Guided Structural Biology, nMS ? SB Resource , is achieved by supporting the TR&D projects, the DBP portfolio, and the Community Engagement mission. The proposed nMS ? SB Resource will develop a native mass spectrometry characterization workflow that will quickly provide structural information on protein complexes that are not amenable to, or not yet at a stage appropriate for, other complementary high- resolution structural biology tools. The data (m/z, stoichiometry, heterogeneity, connectivity, topology, and relative subunit binding strengths of protein complexes) will be acquired relatively quickly, on samples that are not highly purified, and on smaller sample quantities than required for most traditional tools. A broad user community will be trained and results disseminated by presentations, publications, and device installations, with a long-term goal of technology commercialization (integrated surface-induced dissociation with high resolution ion mobility and UV photodissociation). Meeting these combined goals requires effective administration and management as described in the three aims below. ? Aim 1. Define an organizational structure and staff responsibilities that provide scientific leadership, direction, and coordination to foster communication and collaboration among the Resource components. ? Aim 2. Define resource operating procedures, working with the external and internal advisory committees to ensure sound fiscal management and efficient administrative support to all Resource components. ? Aim 3. Assess the effectiveness of the Resource and its progress toward sustainability. Dissemination efforts through training, short courses, workshops, and publications, installations of devices, and vendor commitments to support beta installations and commercialize, are key measures of sustainability.

Project Summary Salmonellosis is one of the most significant food-borne diseases affecting humans and agriculture. Salmonella enterica induces inflammation of the host intestinal tract, which disrupts the normal microbiota. Salmonella then thrives on the nutrients that are not consumed by the microbiota. Salmonella nutrient sources include 1,2- propanediol, which is a product of the microbiota; ethanolamine, which is derived from damaged cells; glucarate and galactarate which are derived from Nos2-mediated oxidation of glucose and galactose; and fructose-asparagine (F-Asn) which is derived from the diet. The F-Asn utilization system provides an interesting therapeutic target as inhibition of the FraB enzyme intoxicates the bacterium with a metabolic intermediate. Our primary objectives are to use a systems-level approach to identify the major nutrient sources utilized by Salmonella over time in the inflamed gut and to identify the microbes that compete for those nutrients. We hypothesize that some of these nutrient acquisition systems will provide therapeutic targets for Salmonella and potentially other Enterobacteriaceae, including the carbapenem-resistant Enterobacteriaceae (CRE) that are classified as an ?urgent? threat by the CDC report, ?Antibiotic resistance threats in the United States?. In other cases, we hypothesize that the competing microbes could be utilized as probiotics or the nutrients utilized could be utilized as prebiotics. We propose to fulfill our objectives and test our hypotheses with the following two aims: 1) Identify the chemical and biological indicators of Salmonella-mediated inflammation over time; 2) characterize metabolic exchanges between Salmonella and its competitors in the gut. The fulfillment of these aims will greatly expand our understanding of the microbial ecology of salmonellosis and may be broadly relevant to other pathogens or related inflammatory disorders.

Abstract The Ohio State University proposes to acquire a UHPLC-Trapped Ion Mobility (IM)-Quadrupole Time-of-Flight mass spectrometer to support the research efforts of NIH-funded users. The proposed instrument, the Bruker timsTOF Pro, was selected because it has several important performance characteristics that meet the challenges of major and minor users described in this application. These advantages expand the capabilities of users to perform clinical and biomedical research where sample amounts are very limited and characterize proteins that have isobaric peptide ?modforms? (distinct patterns of modification for a given peptide sequence). The instrument is unique in several respects: i) ?orthogonal? high resolution IM to achieve separation of coeluting peptide ions (e.g., isobaric peptide modforms), ii) significantly increased sensitivity (50-250 ng of proteins loaded for a typical LC gradient) due to tandem ion trapping with virtually 100% duty cycle, iii) high dynamic range that extends to over 4 orders of magnitude for ion detection, and iv) much faster analysis time (>100 Hz scan acquisition rate). Major users have performed comparisons between existing MS instruments in the core and the timsTOF Pro. For example, analysis of Human histone H4 modifications by major user Freitas yielded greater than twice as many isobaric peptide modforms from the N-terminal tail of H4 when using the timsTOF Pro as compared to the QExactive Plus. The timsTOF Pro also identified peptide sequences absent in the globular domain and C-terminal domain yielding 97% sequence coverage. Similarly, major user Hummon identified double the number of proteins (7,054 versus 3,038) from a mammalian cell lysate without significant benchtop fractionation, due to the ion mobility separation. These results, and several other similar comparisons described in the proposal, show that the timsTOF Pro will provide critically-needed protein identifications to NIH-funded research projects. The proposed instrument will be located in the OSU Mass Spectrometry and Proteomics Facility (MS&P) within the Campus Chemical Instrument Center (CCIC), a campus-wide Center that is administratively managed by the OSU Office of Research. The instrument will be operated by staff of the CCIC MS&P facility and highly trained experts from mass spectrometry labs of selected major-user research groups. The CCIC MS&P Facility is an established, well-utilized, university-wide core and the only proteomics core at OSU. It provides an optimum environment for a state-of-the-art instrument: a vigorous research community with great need for such an instrument and OSU faculty and staff with the expertise and enthusiasm to use the timsTOF Pro to its greatest potential. The requested instrument platform will be invaluable to a very broad constituency of researchers representing 8 NIH institutes.

Abstract. The OSU NIH-funded P41 Resource ?Native Mass Spectrometry Guided Structural Biology? proposes to develop native mass spectrometry (nMS) -based tools for the characterization of protease-resistant protein aggregates/oligomers associated with Alzheimer?s disease and its related dementias (AD/ADRD). The Resource students, postdocs, faculty, and staff have no prior Alzheimer?s disease expertise or funding so this supplemental funding would engage multiple new investigators in AD research, carry the expertise forward as students and postdocs move on to other locations, disseminate the results, and provide a community resource to AD investigators, and their MS core facilities at their local units. The nMS-based tools that currently exist in the P41 and tools under development will be used to tackle the AD problem (nMS coupled to ion mobility and multiple activation methods (surface-induced dissociation, collision-induced dissociation, electron capture dissociation) and covalent labeling methods if needed). In order to study AD related aggregates and oligomers, this supplement proposes purchase of a production model Waters Select Series Cyclic IMS instrument, which will be modified by the Resource to include surface-induced dissociation. The proposed instrument is more sensitive and has higher m/z and ion mobility (IM) resolution than the 8-year-old Waters Synapt Series instruments currently in the Resource. The one-year supplement term will focus on method development on the Cyclic IMS for samples from the Nowick lab at UC Irvine (amyloid beta oligomers and amyloid oligomer mimics) and the Kuret lab at OSU (tau). Additional samples, including brain tissue and antibodies and other probes under development, will be provided by Nowick, Kuret, and collaborators of Kuret who are planning to jointly apply for U24 funding. The Resource will work with investigators to illustrate the complementarity of native MS with other structural biology tools, based on experience developed in ongoing non-AD Driving Biomedical Projects and Collaboration & Service projects. At the end of this development, additional AD investigators will be encouraged to propose to work with the P41 under its Collaborate and Service, Training, and Dissemination missions, to work with one of the external core facilities that have been trained in nMS approaches for AD investigations, or, eventually, to work with the OSU U24 Resource network, if funded. Specific Aims are to develop nMS/IM/MS tools for i) in vitro tau and A? oligomers and A? oligomer mimics, ii) in vitro chemical or molecular probes binding to -oligomers, and iii) aggregates/oligomers and probe-bound oligomers from brain tissue. Developing robust and reliable methods for understanding how both A? and tau aggregate in vitro is essential to better understand the molecular mechanism of AD, and consequently for developing effective diagnostic tools and therapies. Characterization of probe/oligomer interactions and assessing their robustness will establish the utility of these probes for basic science, therapeutic or diagnostic applications.