2020 SUMS-RAS Speakers
MASS SPEC: THE VOYAGE HOME
Wednesday November 16, 2022, 9 am - noon Pacific Time
Dr. Tanveer Singh Batth
Novo Nordisk Foundation Center for Protein Research, University of Copenhagen
High-throughput Ex-vivo Organ Specific Identification of Drug Targets
Proteins are the primary targets of almost all small molecule drugs. However, even the most selectively designed drugs can potentially interfere with a large number of unknown proteins. Current state-of-the-art proteomics methodologies enable screening of 1000’s proteins against a small number of candidate small molecules. However, higher throughput is required in order to determine protein targets of potentially 100’s to 1000’s different small molecules. Here I will present initial results on the development of a label free quantitative proteomics approach, which enables screening of potentially large number of molecules against the proteome in a robust and rapid manner. I will further demonstrate the applicability of this approach by identifying protein targets in various rat organs. Results could prove beneficial for determining physiological outcomes and clinical efficacy of small molecule drugs in humans.
Bio: Tanveer Batth is currently an Assistant Professor at Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen. He has worked in the field of Proteomics for over 10 years covering several different disciplines leading to over 30 high quality publications. His PhD research focused on developing mass spectrometry based phospho-proteomics methodologies to uncover downstream cellular signaling and molecular mechanisms of receptor tyrosine kinases. His research also comprises state-of-the-art proteomics method development such as elucidating the mechanism behind protein aggregation on microparticles which ultimately enable high-throughput proteomics sample preparation. His current research interests span development of chemical proteomics workflows to fungal proteomics for the purpose of characterizing key proteins responsible for post-translation modifications of industrial enzymes. Tanveer aims to be at the leading edge of proteomics for the purpose of elucidating biological mechanisms and function.
Sponsor: ReSyn Biosciences
Dr. Chris Crutchfield
Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine
Cutting-Edge Application Developments in Clinical Mass Spectrometry
Bio: Dr. Christopher Crutchfield is an Assistant Professor in the Department of Pathology and Laboratory Medicine at the University of Cincinnati College of Medicine. He serves as the technical director for the UCHealth Chemistry, Toxicology, and Point-of-Care sections. He is also CLIA medical for the UCHealth Ridgeway Tower Clinical Laboratory, His research interests include mass spectrometry, informatics, and toxicology.
Dr. Lihua Jiang
Department of Genetics, Stanford University
A Quantitative Proteome Map of the Human Body
Determining protein levels in each tissue and how they compare with RNA levels is important for understanding human biology and disease as well as regulatory processes that control protein levels. We quantified the relative protein levels from over 12,000 genes across 32 normal human tissues. Tissue specific or enriched proteins were identified and compared to transcriptome data. Many ubiquitous transcripts are found to encode tissue specific proteins. Discordance of RNA and protein enrichment revealed potential sites of synthesis and action of secreted proteins. The tissue specific distribution of proteins also provides an in-depth view of complex biological events that require the interplay of multiple tissues. Most importantly, our study demonstrated that protein tissue enrichment information can explain phenotypes of genetic diseases, which cannot be obtained by transcript information alone. Overall, our results demonstrate how understanding protein levels can provide insights into regulation, secretome, metabolism, and human diseases.
Bio: Lihua Jiang is trained in medicine and received her Ph.D. in Analytical Chemistry from Dr. Neil Kelleher’s lab in University of Illinois at Urbana-Champaign. After graduation, she worked in Thermo as an application scientist for about two years. When Dr. Michael Snyder, a world-renowned scientist in genomics, transferred from Yale to Stanford, she decided to join force with him in the emerging field of personalized medicine using Omics technology. In Dr. Snyder’s Lab, she built the platform for both proteomics and metabolomics and published her work in the integrated Personal Omics Profiling (iPOP) paper in Cell (2012). In the past a few years, she led the quantitative proteomics study of the normal human tissues as part of the Genotype-Tissue Expression (GTEx) projects. Her work is just published in Cell. She now directs the Mass Spectrometry Center for Advanced Research in the Department of Genetics. She is an expert in mass spectrometry technologies and truly believes that the integration of modern technologies with omics profiling will revolutionize medicine.
Dr. Ulrike Kusebauch
Institute for Systems Biology, Seattle
Discovering Tyrosine Phosphorylation in Mycobacterium tuberculosis
Mycobacterium tuberculosis is the causative agent of tuberculosis, an infectious disease that remains a global health concern. Reversible protein phosphorylation determines growth and adaptive decisions in M. tuberculosis. At least eleven two-component systems and eleven serine/threonine protein kinases mediate phosphorylation on aspartate, histidine, serine, and threonine. However, even after extensive analysis over the years there was no conclusive evidence for protein phosphorylation on tyrosine, and tyrosine phosphorylation was thought to be absent in M. tuberculosis. I will discuss our discovery of the previously unrecognized post-translational modification in M. tuberculosis using a combination of bacterial lysis, phospho-peptide enrichment and highly sensitive mass spectrometry. We conclusively show extensive protein tyrosine phosphorylation of diverse M. tuberculosis proteins including serine/threonine protein kinases.
Bio: Ulrike Kusebauch is a Senior Research Scientist at the Institute for Systems Biology, Seattle, WA. Her research activities include the development and application of proteomic technologies, with a particular focus on targeted proteomics in biomedical research. Dr. Kusebauch studied Pharmaceutical Chemistry and obtained her Ph.D. in Biochemistry at the Max Planck Institute of Biochemistry (Germany). For her postdoctoral work, she joined the group of Prof. Ruedi Aebersold where she contributed to the development of targeted proteomics by selected reaction monitoring (SRM). Dr. Kusebauch continued her research at ISB in the group of Prof. Robert Moritz where she developed complete proteome SRM and SWATH mass spectrometry resources for human and other organisms, and applies quantitative technologies to spatial and temporal proteome dynamics. Dr. Kusebauch received the 2018 HUPO Discovery in Proteomics Sciences Award that recognizes outstanding efforts and achievements of individuals in the field of proteomics.
Sponsor: ReSyn Biosciences
Dr. Jim Prell
Biophysics, Materials Chemistry, Physical Chemistry & Analytical/Bioanalytical Chemistry, University of Oregon
Bio: The Prell laboratory uses state-of-the-art mass spectrometry and ion mobility techniques to investigate the physical and chemical properties that govern the organization of macromolecular assemblies at the nanoscale, including those found in biological membranes. Jim Prell attended college at Washington University in Saint Louis, where he obtained a B.A. in 2005 in chemistry, mathematics, and German, with minors in music and religious studies. He attended graduate school at the University of California, Berkeley (research adviser: Evan R. Williams) and received a Ph.D. in Chemistry in 2011. His research focused on the structure and reactivity of non-covalently bound ions, including ion-biomolecule complexes and extensively hydrated ions. From January 2011 through July 2014, he worked as a post-doctoral scholar at the University of California, Berkeley (research adviser: Stephen R. Leone), studying attosecond-resolved photoelectron imaging of plasmons. He joined the University of Oregon Department of Chemistry and Biochemistry in August 2014, and he is a member of the Materials Science Institute and an associate member of the Center for Optical, Molecular, and Quantum Science. He is the recipient of a 2019 American Society for Mass Spectrometry Research Award and an NSF CAREER Award. Jim is the faculty sponsor for UO’s chapter of the Society for the Advancement of Chicanos/Hispanics and Native Americans in Science. Outside of physical and bioanalytical chemistry, Jim’s interests include classical music performance and composition, running, biking, coffee, cooking, and foreign languages.
Dr. Brandon Ruotolo
Department of Chemistry, University of Michigan
Collision Induced Unfolding: A New Paradigm in Rapid Protein Stability Measurements
Within each living organism proteins are at work, carrying out activities which impact every aspect of cellular function from synthesis to cell death. The next generation of medicines will rely heavily upon our ability to quickly assess the structures and stabilities of such complex macromolecular machines, as well as the influence of large libraries of conformationally-selective small molecule binders and protein-based biotherapeutics. Such endeavours are nearly insurmountable with current tools. In this presentation, I discuss recent developments surrounding collision induced unfolding (CIU) methods to bridge this gap in basic technology. CIU uses ion mobility-mass spectrometry (IM-MS) to measure the stability and unfolding pathways of gas-phase proteins, without the need for covalent labels or tagging, and consuming 10-100 times less sample than almost any other label-free technology. Recent developments in understanding the mechanism of CIU, its ability to differentiate therapeutic antibodies, improving the throughput, and enhancing the information content of such assays will be discussed.
Bio: Brandon T. Ruotolo is currently a Professor in the Department of Chemistry, University of Michigan. He earned his B.S. in Chemistry from Saint Louis University in 1999. Brandon then received his Ph.D. from Texas A&M University in 2004 under the direction of David H. Russell. He did his post-doctoral work at the University of Cambridge with Dame Carol V. Robinson, and was awarded the first ever Waters Research Fellowship in 2008. Brandon moved to the University of Michigan in 2009, where he began his independent career. The Ruotolo research group at the University of Michigan seeks to enable breakthroughs in structural biology and drug discovery by leveraging the potential of ion mobility-mass spectrometry (IM-MS) for the comprehensive, 3D structural analysis of the proteome. To this end, Ruotolo and his team have studied the role of solvation on biomolecular structure, introduced collision induced unfolding (CIU) - a new fingerprinting technology capable of detecting the structural state of protein-ligand complexes and biotherapeutics, developed software packages for the enhanced interpretation and throughput of IM-MS and CIU data, and investigated the structural consequences of small molecule drug-like compounds on amyloid-related peptides. Ruotolo’s work has resulted in ca. 120 peer-reviewed publications, and many awards, including the Eli Lilly Award in Analytical Chemistry, the NSF CAREER award, the ASMS Research Award, the Protein Science Young Investigator Award, and the Agilent Thought Leader Award.
Dr. Miloslav Sanda
Clinical and Translational Glycoscience Research Center, Georgetown University
Structure and Site-specific N- and O- Glycosylation of the SARS-CoV-2 Spike Glycoprotein using Low Collision Energy Fragmentation and Cyclic Ion Mobility
The outbreak of the COVID-19 pandemic is the reason of the current global health crisis. The development of effective antiviral compounds and vaccines requires detailed descriptive studies of SARS-CoV-2 proteins. The SARS-CoV-2 spike (S) protein mediates virion binding to human cells through its interaction with the cell surface receptor ACE2 and is one of the major immunization targets. The functional virion consists of three S1 and three S2 subunits formed by the furin cleavage of the spike protein at R682, a polybasic cleavage site that differs from the animal version of the protein as well as from the SARS-CoV spike protein 2002. We analyzed the glycoprotein using our newly developed methodology based on low-energy fragmentation and cyclic ion mobility. Our analysis confirms the O-glycosylation of the spike protein on a threonine (T678) located near the furin cleavage site. This site is occupied by core-1 and core-2 structures. Two other predicted O-glycosites are unoccupied. We identified eight additional O-glycopeptides on the spike glycoprotein and confirmed that the spike protein is heavily N-glycosylated. We were able to identify LacdiNAc, PolyLacNAc and Sulfated LacdiNAc on several glycosites. In conclusion, our study significantly expands current knowledge of glycosylation of the spike protein and allows the investigation of the effect of O-glycosylation on its proteolytic activation.
Bio: I began my career as a specialist in analytical and bioanalytical chemistry with a special interest in mass spectrometry at the Czech Agriculture and Food Inspection Authority (CAFIA). I was the first to start using the LC-MS methodology for routine measurement of pesticides, mycotoxins and organic pollutants in food and agricultural products at the CAFIA. After my transition to the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of Czech Republic in Prague, I established and led a proteomics subgroup of mass spectrometry team. Since then I have developed and implemented the latest methodology for qualitative and quantitative analysis of proteomics and have collaborated on projects related to cancer biology, virology, enzymology and entomology. In 2010, I began my postdoctoral work at Georgetown University Medical Center concentrating on bioanalytical mass spectrometry in projects in glycobiology and cancer. I have pioneered methodology for site-specific glycosylation analysis based on MRM and DIA technology in biological samples. I currently hold position of Associate Professor and Director of Analytical chemistry of Clinical and Translational Research Center at Georgetown University. My current effort is focused on the structure-specific resolution of glycostructures using mass spectrometry. The subject of studies is to determine glycosylation structure and site-specific glycosylation changes related to cancer, viral disease and immune response. My work is published in 53 peer-reviewed international journals and one patent.
Dr. Kelsi Sandoz
College of Veterinary Medicine, Cornell University
Keeping It All Together: How Mass Spectrometry Revealed a New Tethering Mechanism in the Gram-negative Cell Envelope
Bio: Kelsi Sandoz is an Assistant Professor at Cornell University College of Veterinary Medicine and Director-in-training of the Bacteriology Laboratory at the Animal Health Diagnostic Center. She received her Ph.D. in Molecular and Cellular Biology from Oregon State University and did her postdoctoral training at Rocky Mountain Laboratories (NIAID/NIH) in the laboratory of Dr. Robert Heinzen. During her time at RML she used a new approach to analyze peptidoglycan structure that lead to the identification of a new mechanism of cell envelope stabilization in many proteobacteria. These studies revealed multiple covalent attachments between diverse outer membrane proteins and peptidoglycan. She recently transitioned to a faculty position at Cornell, where she will continue her work on Coxiella burnetii, a highly infectious pathogen that exhibits spore-like environmental stability and extreme resistance to physical stressors during a quiescent physiological state. A central focus of her laboratory will be to explore bacterial cell envelope structure in C. burnetii using MS/MS based approaches, with an aim to build a more complete understanding of structure-function relationships underlying microbial quiescence.
Sponsor: Protein Metrics
Dr. Raghav Sehgal
Section of Endocrinology & Metabolism, Yale University
Drug Metabolism Database: An Integrated Omics Study to Catalogue Metabolic Changes from 500 Drugs, in 50 Different Cell Lines over 5 Years
The mechanism of action of ~20% of FDA approved drugs is unknown. For many more off-target effects remain poorly described. Likewise, compounds orphaned for one indication might have an on or off-target effect that could benefit another indication in mono- or combination therapy. Given the impact, direct or indirect, of pharmaceuticals on metabolism, a curated integrated Omic database to catalogue the metabolic pathway impact of different reagents in different tissues is of significant potential value. With this idea in mind we started the project called Drug Metabolism Database (DMDB) which is an Integrated Omics study to catalogue metabolic changes from 500 drugs, in 500 different cell lines over 5 years. We recently launched the first version of DMDB which has integrative Omics (metabolomic, transcriptomic, fluxomic and phenomic) data from two cell lines (INS and C2C12) cultured overnight in the presence of 10 drugs targeting a wide variety of cellular and metabolic processes. To process data in DMDB we built the AIomic pipeline, an AI enabled integrative Omics pipeline. DMDB, in combination with AIomic, provides a unique platform to find succinct biological insights about drugs using a comprehensive view of metabolism and integration of Omics data, with speed and accuracy.
Bio: Raghav is a PhD student and Gruber Fellow at Yale University. He is an engineer by training. Prior to joining Yale, Raghav was a part of a young Computational Biology and Data Science start-up called Elucidata where he worked as a Data Scientist and Product Manager to build Elucidata's AI enabled drug discovery platforms. Raghav now spends his time understanding metabolism of diseases using integrative Omics and Computational Biology. In a span of just 4 years he has been an author on over 20 posters and over 5 publications in high impact journals such as Nature, Cell Metabolism, Science and more. His most recent work on Drug metabolism database was selected for a talk at ASMS 2020.
Dr. Beatrix Ueberheide
Dept. of Biochemistry and Molecular Pharmacology and Neurology, New York University Langone Health
All Tangled Up: High Resolution Neuroproteomics of the Human pTau Interactome
Bio: Beatrix Ueberheide is the Director of the Proteomics Laboratory and Associate Professor of Biochemistry and Molecular Pharmacology and Neurology at NYU Langone Health. She received her Ph.D. in Chemistry at the University of Virginia with an emphasis on the study of histone post translational modifications using classical ‘Bottom Up’ and ‘Top Down’ strategies under the guidance of Dr. Donald F. Hunt. She joined Rockefeller University for her postdoctoral training in the laboratory of Dr. Brian Chait where she developed de novo sequencing strategies for analysis of venom components and established techniques to study antibodies isolated from individuals. Research in the Ueberheide lab focuses on mass spectrometry-based techniques for a wide range of applications including quantitative proteomics, PTM characterization, epitope mapping, and the characterization of the proteome of neuropathological lesions and distinct cell types using the recently developed ‘localized proteomics’ - Laser Capture Microdissection (LCM) followed by label-free quantitative mass spectrometry (LC-MS).
Sponsor: Protein Metrics
Dr. Balyn Zaro
Department of Pharmaceutical Chemistry, University of California, San Francisco
Proteomic Analysis of Young and Old Hematopoietic Stem Cells and their Progenitors Reveal Unique Post-transcriptional Regulation in Stem Cells
Bio: Balyn Zaro, PhD, grew up in California and Connecticut. As an undergraduate researcher at University of Southern California (USC) she studied synthetic methodology and organic chemistry with G.K. Surya Prakash and Nobel laureate George A. Olah. She remained at USC for her PhD studies in chemical biology as the first graduate student in the laboratory of Matthew Pratt, PhD. Her research focused on developing metabolic bioorthogonal chemical reporters to identify and to characterize post-translational modifications of proteins, including glycosylation, acetylation, and ubiquitination. For her postdoctoral studies, she worked in the laboratory of Ben Cravatt, PhD, at Scripps Research Institute in La Jolla, California. There she investigated the metabolism of covalent small molecules using activity-based protein profiling and identified the mechanisms of action of the multiple sclerosis drug Tecfidera® (dimethyl fumarate). She gained additional training with Irving Weissman, MD, at Stanford University School of Medicine in the fields of innate immunity and hematopoiesis before her arrival at UCSF in September 2019. The Zaro laboratory takes advantage of chemical biology and proteomic techniques to study how protein expression changes during aging, disease, and infection and to develop novel therapeutic interventions in response. They profile how different types of cells metabolize drugs in order to develop more-selective therapeutics for cancer and infectious disease. The Zaro lab also identifies targets critical for modulating the innate immune response during cancer and infection.