SUMS Seminar Series
Deconvoluting Mechanisms of Small Molecules with Mass Spectrometry-based Proteomics
Presented by: Dr. Brendan Dwyer, Ph.D. Postdoctoral Scholar (Nathanael Gray, Dept. of Chemical & Systems Biology, ChEM-H, and Stanford Cancer Institute)
Formalin-fixed and paraffin-embedded (FFPE) tissues represent an invaluable resource for studying molecular mechaSmall molecules serve as invaluable probes to interrogate cellular and pathophysiological systems offering key insight into fundamental biological processes as well as opportunities for therapeutic intervention. Proteomic approaches enabled by mass spectrometry provide an unbiased tool to assess crucial features underlying the molecular mechanisms of chemical probes from target identification to characterizing downstream effects and pathway responses. However, proteomic techniques are often challenging, requiring potentially expensive case-by-case optimization and careful selection of necessary controls and rapidly expanding methodological options across sample preparation, LC-MS/MS data acquisition, and statistical analysis. This talk will feature lessons learned in chemoproteomic-guided mechanism deconvolution of several bioactive small molecules, while providing technical tips and advice. These vignettes include discovering novel targets of clinical-stage drugs and of anticancer natural products as well as developing new therapeutic strategies forchemical inducers of proximity (or molecular glues) that reprogram transcription to selectively kill cancer.
12:00-1:00 pm in Bass Biology Conference Room 122 with lunch provided by Promega
Past Seminars
Ultrasensitive spatial tissue proteomics to assess health and disease
Presented by: Dr. Fabian Coscia, Ph.D. Group Leader, Max Delbrück Center, Berlin
Formalin-fixed and paraffin-embedded (FFPE) tissues represent an invaluable resource for studying molecular mechanisms underlying diseases. The long archival times of FFPE tissue and the fact that proteins are largely stable therein make them ideal analytes for mass spectrometry driven discovery proteomics. Classical approaches have provided “averaged” descriptions of the disease related proteome and fail to characterize the critical disease promoting cell populations within the complex tissue environment. To address this, we have recently co-developed Deep Visual Proteomics (DVP) for image-guided tissue proteomics. DVP leverages high resolution microscopy and machine learning based image analysis to identify phenotypically distinct cell populations. Cells for proteomic profiling, discovered by supervised or unsupervised machine learning, are isolated in situ by automated laser microdissection and analyzed by ultra-sensitive mass spectrometry. In my presentation, I will provide an overview of our spatial tissue proteomics pipeline, discuss our DVP workflow, as well as future applications of tissue proteomics down to a few and even single cells.
1:30-2:30 pm in Bass Biology Conference Room 122 with lunch provided by Bruker
Exhalomics: On-line analysis of metabolites in exhaled breath using ambient ionization mass spectrometry
Presented by: Dr. Renato Zenobi Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
On-line breath analysis is a powerful approach to obtain insight into the metabolism of a person in real time. With ambient ionization methods, this can be achieved rapidly and completely non-invasively, opening up interesting possibilities to diagnose diseases via exhaled breath, to discern diurnal changes in the metabolism, and to monitor drug use (or abuse) by analyzing the chemical composition of exhaled breath.
I will first explain the technical background of secondary electrospray ionization-high resolution mass spectrometry (SESI-HRMS) and discuss the analytical figures of merit (mass resolution, upper mass limit, detection limit, softness of ionization, etc.) as well as the biomarkers (polarity, volatility, molecular weight, etc.) that can be detected. High mass resolution also allows detailed characterization of compounds that can be used as biomarkers, sometimes aided by chromatography, of exhaled breath condensate and comparison against commercially available or synthetic reference compounds. Advances for quantitation of low-level metabolite concentrations in exhaled breath will also be mentioned.
In the second part of the presentation, examples in medical diagnosis, for example, the detection of novel volatile biomarkers for respiratory diseases such as obstructive sleep apnea (OSA), chronic obstructive pulmonary disease (COPD), and cystic fibrosis will be presented. Recent results on monitoring of metabolic changes during sleep, following a nutritional intervention, and of pharmacokinetics via real-time SESI-MS will also be shown.
12:00 - 1:00 pm in Bass Biology Conference Room 122 with lunch provided by ThermoFisher Scientific
Separation of Challenging Citrulline Epimers using SLIM Ion Mobility-Mass Spectrometry (IM-MS)
Presented by: Chris M. Crittenden, Principal Scientist, Synthetic Molecule Pharmaceutical Sciences, Genentech
Experienced Scientist with a demonstrated history of working in the biotechnology industry. Skilled in Mass Spectrometry (MS), Analytical Chemistry, Laboratory Techniques, High-Performance Liquid Chromatography (HPLC), and Laboratory Skills. Doctor of Philosophy (Ph.D.) focused in Analytical Chemistry from The University of Texas at Austin.
Meenakshi Goel, Scientist 3, Synthetic Molecule Pharmaceutical Sciences, Genentech
12+ years of pharma experience in analytical, organic and peptide chemistry. Support research, development and clinical testing of bio-therapeutics using state of the art analytical techniques like High pressure Liquid Chromatography (HPLC), Gas Chromatography (GC), Supercritical Fluid Chromatography (SFC), light scattering and hyphenated techniques including High resolution LC-MS, 2D-LC, 2D-LC-SFC, and Ion Mobility (IM). With the recent advancement in ion mobility technology and instrumentation our lab is exploring the capabilities of SLIM Ion Mobility Mass Spectrometry to solve some of the challenging analytical problems including separation of epimers, atropisomers, and conformers of synthetic peptides.
12:00 - 1:00 pm in Bass Biology Conference Room 102 with lunch provided by Mobilion Systems
Evolving MS Technologies for Advancing Biomedical Applications
We are pleased to present a three-part series on new techniques and technologies that are enabling the next wave of scientific exploration using mass spectrometry. First, Dr. Richard Lock will share details on a new MS platform - the Waters Xevo MRT - which offers a high scanning speed for complex mixtures of small molecules, peptides, and lipids without compromising on resolving power. Dr. Lock is the Director of Discovery and Characterization at Waters Corporation, where he oversees a team of scientists and product managers responsible for Waters' benchtop QTOF instruments, including the Xevo™ G3 QTOF mass spectrometer and the Waters Xevo MRT next-generation technology. Next, Dr. Andy Baker will share new research results on targeted mapping of lipids in the brain using desorption electrospray ionization tandem MS. Dr. Baker is a Consulting MS Applications Scientist at Waters focusing on LC/MS/MS and LC/IMS/MS techniques, and completed this study in collaboration with both SUMS and Dr. Marios Georgiadis in the Department of Radiology at Stanford University. Finally, Dr. Byungjin Lee from the Fordyce Laboratory will share his recent developments in using desorption electrospray ionization MS capabilities at SUMS.
Richard Lock PhD: Director of Discovery and Characterization, Waters
Andy Baker PhD: Mass Spectrometry Applications Scientist, Waters
Byungjin Lee PhD: Postdoctoral Fellow, Fordyce Laboratory, Stanford University
11:30 am - 1:30 pm in Bass Biology Conference Room 102 with lunch provided by Waters Corporation
Multimodal imaging methods for understanding complex biological phenomena
Organ systems are composed of unique cell types that actively coordinate to enable higher order functions. Even slight deviances in the molecular or cellular states of these systems can result in debilitating disorders whose severity, treatment course, and overall treatment outcome vary widely from patient to patient. This level of complexity likely contributes to promising therapeutics failing within clinical trials and, thus, require further exploration. Thus, the Neumann lab focuses on developing and applying multimodal imaging and profiling techniques to study the molecular and cellular architecture behind complex human diseases, such as renal cell carcinoma, Alzheimer’s Disease, and Canavan’s Disease. To do this, we combine multiple analytical tools to detect molecules throughout the central dogma of biology, including genes, proteins, and metabolites. Our main instrument is the Bruker timsTOF fleX MALDI MS system, which enables us to detect hundreds to thousands of metabolomic features at <10 µm spatial resolution. In conjunction with immunohistochemistry and spatial transcriptomics, we can connect these metabolomic profiles to specific cell types and cell states. These integrated technologies can be used on a variety of biological samples with high reproducibility and rigor.
Elizabeth Neumann PhD: Assistant Professor, Department of Chemistry, UC Davis
12 - 1 pm in Bass Biology Conference Room 122 with lunch provided
Pioneering the Next Generation of Mass Spectrometry-Based Plasma Proteomics Biomarker Study
Analyzing biomarkers in plasma offers a minimally invasive and accessible method for disease diagnosis, including early cancer detection and translational medicine research. Untargeted proteomic mass spectrometry (MS) utilizing data independent acquisition (DIA) provides an unbiased, precise, and accurate approach to interrogate the human plasma proteome. However, plasma proteomics has historically been challenging due to sample complexity, instrument sensitivity, depth of coverage, and scalability. Recent advances in nanoparticle sample preparation with the Seer ProteographTM and MS instrumentation (i.e. Bruker timsTOF HT, Sciex ZenoTOF and Thermo Astral) have enabled the detection of thousands of proteins at high throughput, which is enabling a new era in plasma proteomics. Through a combination of our prospectively collected multi-cancer cohort, ProteographTM, orthogonal peptide fractionation techniques and the latest MS instruments, we have generated the deepest plasma proteomics spectral libraries to date. The impact of these new libraries was demonstrated by application to one of our previous multi-cancer studies, which resulted in a 2x increase in protein groups. As a demonstration of the capabilities of these technologies, we’ve conducted an untargeted biomarker study on ~3,000 subject multi-cancer cohort using multiple EvosepOne and timsTOF HT instruments. Across 2470 subjects, we’ve detected 8,335 protein groups (PGs) and 113,634 peptides at high throughput & precision. Among those identified PGs in the study, we’ve further investigated the statistic significancy of protein group level detected across 5 nano particles between different cohort conditions.
Jimmy Yi Zeng PhD: Associate Director of Mass Spectrometry, prognomiQ
12 - 1 pm in Bass Biology Conference Room 122 with lunch provided
Systematic mapping of the human cell surface proteome using proximity labeling and quantitative proteomics
The human cell surface is a highly heterogenous environment that harbours proteins critical for immune cell activation, cell-cell interactions, and cellular signaling among many other tasks. Despite the importance of proteins found on the cell surface, comprehensive analyses of the cell surface proteome have been lacking. Using a combination of proximity labeling approaches and an optimized DIA mass spectrometry workflow for quantitative proteomics we have developed an approach for identifying and determining the arrangement of cell surface proteins in a systematic manner. Overall, this approach grants the opportunity to probe functional clusters on the cell surface and provides insight for informed cell surface engineering.
Brendan Floyd PhD: Postdoctoral Scholar-Bertozzi Lab, Department of Chemistry at Stanford University
12 - 1 pm in Bass Biology Conference Room 122 with lunch provided
Answering what and where in complex samples: Advances in Imaging mass spectrometry and the impact of high-resolution mass measurement and ion mobility
This discussion will cover the advances in Imaging mass spectrometry techniques and technology using practical examples of molecular discovery and quantitation. We’ll cover ionization techniques, analysis tools and data pipelines that match spatial features on tissue with chemical signals like drugs and metabolites and potential biomarkers.
Roy Martin, PhD - Principal Field Marketing Manager for Biological Mass Spectrometry at Waters Corporation
12 - 1 pm in Bass Biology Conference Room 122 with lunch provided
Structural characterization of lipids using electron-activated dissociation (EAD): From plasma analysis to improved quantitative measurements
The analysis of lipids by mass spectrometry is the foundation of modern lipidomics. Using electrospray ionization (ESI), most lipids can be readily quantified in targeted assays. However, discovery experiments, such as data-dependent acquisition (DDA) methods, have proven to be more difficult to achieve in terms of specificity and structural characterization. This challenge arises from the extensive inter- and intra-molecular isobaric overlap among lipids. Collision-induced dissociation (CID), the primary fragmentation method used for lipid analysis, generates few diagnostic ions other than the lipid head group and the acyl chains, which are fragments often shared among isobars. Consequently, discovery experiments generally identify lipids at the sum composition or fatty acid level, which lack structural specificity. Recent advances in mass spectrometry have produced an alternative fragmentation mechanism, EAD, that provides structurally diagnostic fragment ions to enable the complete characterization of a lipid molecule by mass spectrometry.
In this seminar, the use of EAD to fully characterize lipids structurally will be demonstrated using the SCIEX ZenoTOF 7600 system. This instrument has a tunable electron beam to produce fragments from singly charged lipids that can be used to identify lipids by their class, fatty acid composition, fatty acid position, double bond position(s) and double bond stereochemistries. These data enable the complete structural identification of lipid molecular species. The results presented will demonstrate that this level of characterization can be achieved on a liquid chromatography (LC) time scale, which enables high-throughput data acquisition in samples of diverse origins. The basic mechanisms of lipid fragmentation will be discussed using human plasma as an example but the use of this technique extends beyond traditional discovery experiments to quantitative applications that leverage EAD to increase the speed and specificity of assays. The data presented will show that the ZenoTOF 7600 system with EAD is uniquely capable of the specific structural identification of lipid molecular species in simple and complex matrices.
Paul RS Baker, PhD - Senior Staff Scientist at Sciex
12 - 1 pm in Bass Biology Conference Room 122 with lunch provided
Leveraging proteomics for biomarker and pathway discovery in neurodegeneration
Neurodegeneration is a broad set of complex diseases that are increasingly associated with genetic risk factors related to cellular homoeostasis, lysosomal function, and glial biology in the brain. The difficulty in developing therapeutics targeting these diseases necessitates tools to probe the increasingly novel biology and complex interplay between normal and pathological function at the protein level. Recent advances in mass spectrometry instrumentation have brought unparalleled increases in speed, sensitivity and capability that has unlocked new opportunities for proteomics in therapeutic research and biomarker discovery. I will discuss how we have set up and utilized the timsTOF platform to expand our proteomics capabilities with increased depth and reproducibility and how we support discovery biology and biomarker programs.
Neal Gould, PhD - Principal Proteomics Scientist, Denali Therapeutics
12 - 1 pm in Bass Biology Conference Room 122 with lunch provided
Next-generation Protein Sequencing™: Understanding single-molecule amino acid changes with Platinum™
Next-generation protein sequencing on Platinum enables individual amino acid interrogation with the use of semiconductor chips and fluorescently labeled-n-terminal amino acid recognizers, which leads to deeper understanding of proteins and their impact on cell function.
David Dickey, PhD - Senior Field Applications Scientist, Quantum-Si Inc.
12 - 1 pm in Bass Biology Conference Room 122 with lunch provided
Answering what and where in complex samples: Advances in Imaging mass spectrometry and the impact of high-resolution mass measurement and ion mobility
This discussion will cover the advances in Imaging mass spectrometry techniques and technology using practical examples of molecular discovery and quantitation. We’ll cover ionization techniques, analysis tools and data pipelines that match spatial features on tissue with chemical signals like drugs and metabolites and potential biomarkers.
Roy Martin, PhD - Principal Field Marketing Manager for Biological Mass Spectrometry at Waters Corporation
12 - 1 pm in Bass Biology Conference Room 122 with lunch provided
Structural characterization of lipids using electron-activated dissociation (EAD): From plasma analysis to improved quantitative measurements
The analysis of lipids by mass spectrometry is the foundation of modern lipidomics. Using electrospray ionization (ESI), most lipids can be readily quantified in targeted assays. However, discovery experiments, such as data-dependent acquisition (DDA) methods, have proven to be more difficult to achieve in terms of specificity and structural characterization. This challenge arises from the extensive inter- and intra-molecular isobaric overlap among lipids. Collision-induced dissociation (CID), the primary fragmentation method used for lipid analysis, generates few diagnostic ions other than the lipid head group and the acyl chains, which are fragments often shared among isobars. Consequently, discovery experiments generally identify lipids at the sum composition or fatty acid level, which lack structural specificity. Recent advances in mass spectrometry have produced an alternative fragmentation mechanism, EAD, that provides structurally diagnostic fragment ions to enable the complete characterization of a lipid molecule by mass spectrometry.
In this seminar, the use of EAD to fully characterize lipids structurally will be demonstrated using the SCIEX ZenoTOF 7600 system. This instrument has a tunable electron beam to produce fragments from singly charged lipids that can be used to identify lipids by their class, fatty acid composition, fatty acid position, double bond position(s) and double bond stereochemistries. These data enable the complete structural identification of lipid molecular species. The results presented will demonstrate that this level of characterization can be achieved on a liquid chromatography (LC) time scale, which enables high-throughput data acquisition in samples of diverse origins. The basic mechanisms of lipid fragmentation will be discussed using human plasma as an example but the use of this technique extends beyond traditional discovery experiments to quantitative applications that leverage EAD to increase the speed and specificity of assays. The data presented will show that the ZenoTOF 7600 system with EAD is uniquely capable of the specific structural identification of lipid molecular species in simple and complex matrices.
Paul RS Baker, PhD - Senior Staff Scientist at Sciex
12 - 1 pm in Bass Biology Conference Room 122 with lunch provided
Leveraging proteomics for biomarker and pathway discovery in neurodegeneration
Neurodegeneration is a broad set of complex diseases that are increasingly associated with genetic risk factors related to cellular homoeostasis, lysosomal function, and glial biology in the brain. The difficulty in developing therapeutics targeting these diseases necessitates tools to probe the increasingly novel biology and complex interplay between normal and pathological function at the protein level. Recent advances in mass spectrometry instrumentation have brought unparalleled increases in speed, sensitivity and capability that has unlocked new opportunities for proteomics in therapeutic research and biomarker discovery. I will discuss how we have set up and utilized the timsTOF platform to expand our proteomics capabilities with increased depth and reproducibility and how we support discovery biology and biomarker programs.
Neal Gould, PhD - Principal Proteomics Scientist, Denali Therapeutics
12 - 1 pm in Bass Biology Conference Room 122 with lunch provided
Next-generation Protein Sequencing™: Understanding single-molecule amino acid changes with Platinum™
Next-generation protein sequencing on Platinum enables individual amino acid interrogation with the use of semiconductor chips and fluorescently labeled-n-terminal amino acid recognizers, which leads to deeper understanding of proteins and their impact on cell function.
David Dickey, PhD - Senior Field Applications Scientist, Quantum-Si Inc.
12 - 1 pm in Bass Biology Conference Room 122 with lunch provided
Thursday July 20, 2023
Noon - 1 pm
Bass Biology Conference Room 122
Daniel Hornburg, PhD - Vice President of R&D and Tech Development, Seer Inc.
Deep and Scalable Discoveries in the Human Plasma Proteome
Thursday March 16, 2023
Noon - 1 pm
Bass Biology Conference Room 122
Lunch provided
Roy Martin, PhD - Senior Manager for Biological Mass Spectrometry, Waters Corporation
Advances in Imaging Mass Spectrometry: enabling faster and in-depth analysis of lipids and metabolites using MALDI and DESI
Imaging mass spectrometry is driven by the need to spatially locate molecules of interest in biologically relevant materials such as biopsies and tissue. Rapid development in the sample preparation, ionization techniques and methodologies and new Mass Spec technology have opened up many new avenues of analysis. Both MALDI and DESI have long been available as ionization modes for imaging and direct sample analysis and now DESI has only been recently developed to match the robustness and simplicity of MALDI methods. This presentation will investigate the state of the art of these two ionization techniques, how they differ and where they might be most applicable. With recent advances similarities in sensitivity (compound specific) and spatial resolution the choice between these can distill down to the consideration of specific chemistry required, the speed of the analysis and the tissue or matrix type.
Dr. LeRoy B. Martin, III is a Senior Manager for Biological Mass Spectrometry at Waters Corporation. He received a BS in Chemistry from Davidson College in Davidson, NC, and a PhD in Analytical Chemistry from North Carolina State University in Raleigh, NC. At Waters, Roy has been part of the development of the Omics and biological research program since starting in 1992. Currently, his primary role is developing and implementing advanced mass spectrometry solutions in the Americas. He is currently managing the Biomolecular Research marketing effort in the Americas. He is also charged with evaluating and integrating new technologies and planning for their inclusion either as Waters Corp. offerings or in combinations of instrumentation platforms. Recently he’s been particularly focused on the ion mobility, imaging, and direct analysis platforms and integrating these technologies into a molecular discovery platform.
Thursday May 12, 2022 - SUMS Seminar Series
Daojing Wang, PhD - Founder & CEO, Newomics Inc.
Silicon Microfluidic Chip Platform for Proteomics
Proteomics of small volumes of biological samples down to single cells has progressed rapidly. However, simultaneous achievement of sensitivity, reproducibility, and throughput for LC-MS-based proteomics remains a challenge. Newomics silicon-microfluidic-chip platform has been demostrated to provide novel solutions to address the challenge. Two products will be introduced in this seminar. The first is the M3 emitter, a multinozzle emitter that enables microflow LC-nanospray ESI-MS, which achieves the robustness and throughput with microflow LC, while maintaining the sensitivity of nanoflow ESI-MS. The second is the MEA chip that monothically integrates the M3 emitter with an on-chip LC column, thereby reducing the dead volume and simplifying the plumbing and connection for nanoflow LC-MS. Applications in bottom-up, targeted, and top-down proteomics, as well as native MS analysis of proteins and protein complexes, will be showcased.
View recording
Thursday May 5, 2022 - SUMS Seminar Series
Daniel Hornburg - Senior Director, Discovery, Research and Tech Development, Seer Inc.
Optimized nanoparticle-based plasma proteomics with enhanced scale, precision, and depth of coverage for low abundant protein biomarkers
Intriguingly, most FDA approved biomarkers in blood are high-abundance proteins. Considering that in biology, the utility of quantifying a protein is not expected to be a function of its abundance, this suggests that many biomarkers are yet to be discovered among hard-to-detect, low-abundance proteins. To overcome the current limitation of a deep, unbiased access to the plasma proteome at population scale, we developed a fast and scalable technology that leverages protein-nano interactions. Introducing nanoparticles (NPs) into a biofluid such as blood plasma leads to the formation of selective, specific, and reproducible protein coronas driven by protein-NP affinities, protein abundances, and protein-protein interactions. Importantly, in contrast to targeted approaches, NPs leverage combinations of multiple generic affinities, which across a panel of engineered NPs compress the entire dynamic range enabling quantitative detection of known as well as novel protein variants. We will discuss how combining nanotechnology, biochemistry, mass spectrometry and data science will advance our understanding of the molecular landscape of health and disease and how machine learning can dissect nano-bio interactions to guide the NP engineering process.
Thursday April 28, 2022 - SUMS Seminar Series
Connecting LC-MS data analysis with non-MS techniques to provide deeper insights
Eric Carlson, PhD - CEO, Protein Metrics
In person and online:
Bass Biology conference room 122 / Zoom webinar, noon-1 pm
Lunch provided by Protein Metrics
LC-MS data is central to protein characterization and to proteomics research, but it never stands alone. Decisions are made and insights are gained when these data are reviewed in the context of other experimental techniques and meta data related to the sample and the experiment. In this talk, Dr Carlson will review recent updates to the Protein Metrics platform and talk about the “next steps” of informing MS-level experiments with information from biology and process, as well as what all mass spectrometrists already proclaim, that we can inform biology in reverse.
Thursday April 21, 2022 - SUMS Seminar Series
Optimizing Proteolysis for Improved Coverage of Challenging Proteins
Norah Brown, MS - Stanford University
In person and online:
Bass Biology conference room 122 / Zoom webinar, noon-1 pm
Lunch provided by Promega
Proteomics mass spectrometry is a powerful tool to characterize various disease states at a molecular level, especially when biological material is in ready supply. However, many investigations remain challenging when they are limited by the types of peptides which are readily detected for proteins of interest. There is increasing need for experimental methods which are capable of detecting specific classes of proteins or post translational modifications efficiently with high throughput. For example, while trypsin remains the standard protease used for discovery proteomics, it can perform poorly depending on the amino acid composition of a target protein. Furthermore, the impact of pH and heat on the stability of trypsin creates a significant bottleneck in the sample preparation pipeline at clinical scale. ProAlanase is a protease that has high proteolytic activity in acidic conditions and digestion times under 2 hours. This enzyme has high specificity for proline and alanine, which has the capability to profile characteristics of histones where lysines and arginines are often modified, membrane-bound proteins which often lack these residues, and other proteins and protein regions which are not readily observed with trypsin. This protease can be used independently, or if sufficient sample is available as a complementary choice to trypsin, and assist in de-novo sequencing or phosphorylation site localization of proteins with proline-rich regions. Here, we optimize proteomic sample preparation to improve throughput for multi-protease analyses by decreasing incubation times for reduction, alkylation, and digestion. Furthermore we investigate the benefits of using ProAlanase as both a complementary and an alternative protease for bottom-up proteomics and peptide mapping. This approach enables rapid digestion of samples and complementary sequence coverage of proline and alanine containing proteins.
Thursday October 1, 2020 - SUMS Seminar Series
Reasons to be excited about current efforts in glycoproteomics
Nick Riley, PhD - Dept. of Chemistry, Stanford University
Zoom webinar, noon-1 pm
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Glycoproteomics is a rapidly developing field, driven by improvements in sample preparation, instrumentation, and post-acquisition software. Recent years have ushered in a wave of new glycoproteomics studies, both as mass spectrometrists learn how to best apply their expertise to the needs of glyco-analysis and as MS methods become more democratized for glycobiologists to use. Here we will cover new developments in 1) preparation of glycoproteomic samples, 2) quantitation strategies used for glycopeptide characterization, 3) the most useful data acquisition strategies for various types of glycopeptides, 4) software for interpretation of glycopeptide spectra, and 5) tools for data visualization and meta-analysis. It will be difficult for this overview to be truly comprehensive or thoroughly detailed, but the hope is that this discussion will provide a springboard to generate more interest in glycoproteomic advances and will point interested parties to relevant starting points for continued learning.
Thursday September 24, 2020 - SUMS Seminar Series
The role of host arginases in murine malaria
Nicole Davis, PhD - Dept. of Microbiology & Immunology, Stanford University School of Medicine
Zoom webinar, noon-1 pm
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Malaria, a deadly disease caused by Plasmodium parasites, remains a global health threat. Vascular distress in malaria is thought to be caused by depletion of the vasodilator nitric oxide and its amino acid precursor arginine. Arginine is depleted in the plasma of malaria patients, but the causes of hypoargininemia remain incompletely understood. We sought to determine the cause(s) of arginine deletion in a Plasmodium chabaudi murine model of malaria. In a metabolic survey of P. chabaudi-infected mice, we noted an inverse relationship between plasma arginine and alanine aminotransferase (ALT), a plasma marker for hepatocellular injury. Injured hepatocytes also release arginine-consuming arginase-1 (Arg1) into circulation, which suggested that hepatic Arg1 could deplete arginine following malaria-induced liver injury. We used computational and host genetic tools in combination with LC-MS to test the extent to which hepatic Arg1 and other host arginases deplete plasma arginine during malaria. We found that hepatic Arg1 provided a partial explanation for arginine depletion in P. chabaudi infection, and it may explain arginine depletion in some human populations. Collectively, our work motivates increased attention to the role of malarial liver damage in disrupting host arginine metabolism.
Thursday September 3, 2020 - SUMS Seminar Series
Fundamentals: An introduction to MS-based glycoproteomics
Nick Riley, PhD - Dept. of Chemistry, Stanford University
Zoom webinar, noon-1 pm
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Protein glycosylation is a prevalent, yet heterogeneous co- and post-translational modification (PTM). Glycosylation mediates biophysical and biochemical interactions both intra- and extracellularly, with roles ranging from structural stability, immune regulation, cell proliferation, and intercellular dynamics (to name a few). Similar to other PTMs, e.g., phosphorylation and acetylation, mass spectrometry is the premier method to map site of glycosylation, but challenges inherent to the heterogeneity of glycosylation (in both the glycans that modify proteins and the sites that are modified) make glycoproteomics significantly more difficult. Here we will discuss fundamental mental characteristics of several classes of protein glycosylation, including N-glycosylation and two different types of O-glycosylation (O-GlcNAc vs. mucin-type/O-GalNAc). We will also cover standard workflows used in the field, covering protease considerations, enrichment options, LC-MS/MS methods, and well-established analysis tools. Importantly, we will address shortcomings and challenges that remain in glycoproteomics, too. Glycoproteomics data will be discussed in context with other -omics efforts, e.g., glycomics and standard proteomics, with the ultimate goal that MS researchers unfamiliar with the glyco world will be able to appreciate nuances required in glycosylation analysis.
Thursday July 23, 2020 - SUMS Seminar Series
Mass Spec Fundamentals: what you didn’t know you needed to know
Speaker: Ryan Leib, PhD
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An encore performance of the inaugural seminar of our Fundamentals Series! In case you missed it in-person, we are streaming and recording this essential presentation. This seminar will cover the basic foundations of ion generation, manipulation, and detection in a typical LC/MS experiment, and why it matters to your research. This is a great jumping on point for scientists new to mass spectrometry who are excited to learn a bit about the underlying physical processes that make these experiments possible.
Thursday October 15, 2020 - SUMS Seminar Series
Calcineurin phosphatase activity regulates Varicella-Zoster Virus induced cell-cell fusion
Momei Zhou, PhD - Dept. of Pediatrics, Stanford University School of Medicine
Zoom webinar, noon-1 pm
View recorded webinar
Download .pdf of slides *** MISSING DOWNLOAD FILE ***
Cell-cell fusion (abbreviated as cell fusion) is a characteristic pathology of medically important viruses, including varicella-zoster virus (VZV), the causative agent of chickenpox and shingles. Cell fusion is mediated by a complex of VZV glycoproteins, gB and gH-gL, and must be tightly regulated to enable skin infection. Although the function of gB and gH-gL in the regulation of cell fusion has been explored, whether host factors are directly involved in this regulation process is unknown. Here, we discovered host factors that modulated VZV gB/gH-gL mediated cell fusion via high-throughput screening of bioactive compounds with known cellular targets. Calcineurin, a cellular phosphatase, was singled out for study and was demonstrated to regulate gB/gH-gL mediated cell fusion via compounds that bind to FKBP1A, which specifically inhibit calcineurin phosphatase activity, led to remarkably enhanced cell fusion. Consistent with a broad role in fusogen modulation, inhibition of calcineurin phosphatase activity enhanced both herpes simplex virus-1 and synctin-1 mediated cell fusion. Further supporting the role of calcineurin phosphatase activity, inhibitor-induced enhanced cell fusion was significantly reduced by FKBP1A knockdown. Importantly, inhibition of calcineurin phosphatase activity during VZV-infection caused exaggerated syncytia formation and suppressed virus propagation, which was consistent with previous studies. Phosphopeptide enrichment and Orbitrap mass spectrometry identified seven host cell proteins that remained uniquely phosphorylated when calcineurin phosphatase activity was inhibited. This suggests that the dephosphorylation of one or more of those seven proteins is required for calcineurin-dependent fusion regulation. These findings demonstrate that calcineurin is a critical host cell factor pivotal in the regulation of VZV induced cell fusion, which is essential for VZV pathogenesis.
Thursday July 9, 2020 - SUMS Seminar Series
Improved protein and PTM characterization with a practical electron-based fragmentation on Q-ToFs and ion mobility separations
Joe Beckman, PhD - Distinguished Professor of Biochemistry, Oregon State University, CEO of e-MSion, Inc.
Zoom webinar, noon-1 pm
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Electron-induced fragmentation (ExD) is well known to produce uncluttered spectra of entire proteins with labile post translational modifications preserved, but has not been practical in most mass spectrometers. We have developed an efficient ExD device that can be retrofitted into Q-ToFs and Orbitrap QE instruments. Once the ECD cell has been optimized to maximize fragmentation of small peptides like substance P, the same parameters also work with slight adjustments for fragmenting native and unfolded proteins. Nearly complete sequence coverage was obtained with “native”-folded proteins. ECD also efficiently cleaves disulfide bonds within proteins to increase coverage. Sequence coverage of 80-95% was obtained for small proteins like ubiquitin and a-synuclein (14 kDa) during UPLC separations from chromatographic peaks lasting 3-5 seconds. For carbonic anhydrase (29kDa), sequence coverage as 93% (half of the human proteome is smaller than 30kDa). Approximately 90% sequence coverage for each of the three subunits from 0.1 ug of an IdeS-digested antibody was obtained in a five-minute nanoflow separation. The protein spectra consisted primarily of c and z ions, though the ECD cell also produced a substantial number of d and w sidechain fragments. These side-chain fragments allow leucine/isoleucine and isoaspartate/aspartate pairs to be distinguished, which facilitates de novo sequencing. Labile post-translational modifications are also retained, including phosphorylation, glycation and deuterium incorporation. Deuterium labeling of ubiquitin enabled top-down hydrogen/deuterium exchange with residue-specific resolution at rates consistent with NMR. The copper and zinc cofactors in superoxide dismutase (17 kDa) remained bound to their respective binding sites in ECD fragments. The simplified fragmentation patterns made possible with the ExD cell allows existing mass spectrometers to characterize mid-sized proteins even using fast front-end separations including ion mobility separations. Because the ExD cell supports collisional ion activation and unfolding, more complete sequence coverage can be achieved for large native protein complexes than previously possible on any instrument.
Thursday July 9, 2020 - SUMS Seminar Series
In-depth shotgun triacylglyceride profiling
Matias Cabruja, PhD - Dept. of Genetics, Stanford University School of Medicine
Zoom webinar, noon-1 pm
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Triacylglycerides (TAG) levels are associated with metabolic (e.g. diabetes) and cardiovascular diseases. TAG detailed analysis might be important to better understand their biological properties and their roles in health and disease states. Comprehensive TAG content characterization is methodologically challenging due to the high complexity and similarity. Current high-throughput targeted methods only inform on one fatty acid chain while single species quantification requires extensive LC separations or highly sophisticated (Tribrid) spectrometers. We have developed a high-throughput method to quantify individual TAG species using shotgun MS3.
Brought to you in conjunction with Sciex
Thursday July 2, 2020 - SUMS Seminar Series
Fundamentals: Bioanalytical LC/MS method validation -- fit for purpose
Ludmila Alexandrova, PhD
Zoom webinar, noon-1 pm
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With the increasing importance of research reproducibility and requirements of peer-reviewed scientific journals, the reliability of bioanalytical data and the value of method validation cannot be underestimated. Unreliable results are subject to misinterpretation and can lead to project failure. At the same time, extensive method validation is a complicated and time-consuming process and is not to be undertaken lightly. This seminar will provide an overview of validation guidelines, requirements, approaches, workflow, and data analysis. Case studies will illustrate the fit-for-purpose concept -- suiting the level of validation to the intended purpose of the study. Please bring your questions and suggestions.
Thursday June 25 - SUMS Seminar Series
ASMS review: recap the reboot!
Zoom meeting, noon-1 pm
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What caught your eye at ASMS? What are your take-homes? Which presentations would you recommend to others? Join us to recap the reboot -- compare notes, share highlights, and discuss developments of interest. With recorded content online until August 31st, get the inside scoop on which sessions to watch on-demand.
June 1-19, 2020 - ASMS & Short Courses
Seminar series is on hiatus during the online ASMS Reboot
Thursday May 28, 2020 - SUMS Seminar Series
Mass spec bloopers! And other amusing adventures
The lighter side of mass spec. A collection of the weird and the wonderful -- we couldn't make this stuff up if we tried!
Hear from our intrepid crew:
- David Quilici, University of Nevada, Reno
- Brett Phinney, University of California, Davis
- Kimberly Lee, Cell Signaling Technology
- Toni Koller, Massachusetts Institute of Technology
- Allis Chien, Stanford University
Zoom meeting, noon-1 pm
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Thursday May 21, 2020 - SUMS Seminar Series
Fundamentals: Applications of LC/MS in small molecule drug discovery
Liquid chromatography-mass spectrometry (LC/MS) is a proven technique of choice for many assays implemented during the various stages of drug discovery and development. Join us for an overview of LC/MS applications in the drug discovery process with emphasis on metabolism and pharmacokinetic studies. We will share real-world project examples with focus on selection of suitable LC/MS instrumentation, method development approaches, sample preparation, data analysis and interpretation.
Ludmila Alexandrova, PhD
Zoom webinar, noon-1 pm
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Thursday May 14 2020 - SUMS Seminar Series
Breakout discussion topics:
- Implementing new technologies & techniques
What new areas are looming on your horizon? Think and talk through approaches to selecting, testing and onboarding new methods in a core lab environment.
- Folk wisdom: sample prep, instrument operations, data analysis
The devil is in the (unpublished) details! Share best practices for the various stages of a mass spec experiment, both in and out of the lab.
- Research restart in the COVID-19 era
During the unfolding COVID-19 situation, universities including Stanford have ceased non-essential research activities. As we prepare to return to the lab, this forum will be an opportunity to discuss changed workflows, new laboratory safety measures, and phased research restart strategies.
Bring your questions, share your experiences, and learn from each other in the hosted breakout discussions; then rejoin everyone in the main meeting room for a report back on key points from each of the discussions. Note: the breakout room discussions will not be recorded; the summary reports to the recombined group will be recorded and made available here.
Speakers: you, and many others!
Zoom meeting, noon-1 pm
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Thursday May 7, 2020 - SUMS Seminar Series
Fundamentals: Native mass spectrometry & relevant techniques
Beryl Xia, PhD
Zoom webinar, noon-1 pm
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Interested in using mass spectrometry as a tool for structural biology? Curious about emerging approaches for protein research? This seminar will provide a broad overview of native mass spectrometry and its applications, and touch on both popular and non-commercial emerging techniques relevant to native mass spectrometry. Topics include charge detection mass spectrometry (CDMS), ion mobility spectrometry (IMS), hydrogen-deuterium exchange (HDX), and more.
Thursday April 30, 2020 - SUMS Seminar Series
Fundamentals: Peptide quantitation strategies
Fang Liu, PhD; Beryl Xia, PhD
Zoom webinar, noon-1 pm
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A deeper dive into quantitation techniques specifically for peptides, including selected reaction monitoring (SRM), parallel reaction monitoring (PRM), TOMAHAQ, SureQuant, and more.
Thursday April 23, 2020 - SUMS Seminar Series
Fundamentals: Measuring concentrations of small molecules using mass spectrometry - theory and practice, part II
Karolina Krasinska, MS
Zoom webinar, noon-1 pm
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Part II, with emphasis on the practice: How can I measure concentrations of specific molecules in my sample? What are the possible approaches and how do I determine which one is best for my application? What do I need to consider when planning such a project? This seminar will answer these questions and more, explaining mass spectrometry-based targeted quantitation from the ground up. Learn about common pitfalls and strategies to navigate around them. Gain practical tips on data analysis and what your data can and can’t tell you. Bring your questions, learn from your fellow researchers’ questions, and come away with a solid grounding in this core analytical technique.
Thursday April 16, 2020 - SUMS Seminar Series
Fundamentals: New proteomic approaches and essential data handling tips
Kratika Singhal, MS; Rowan Matney, BA
Zoom webinar, noon-1 pm
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Get the inside scoop on both ends of proteomic workflows: from sample prep approaches for experiments like TMTPro-16plex, phosphoproteomics and SureQuant, to what to do with your data once the results are in.
Thursday April 9, 2020 - SUMS Seminar Series
Fundamentals: Intact protein mass spectrometry - tips and best practices
Theresa McLaughlin, MS
Zoom webinar, noon-1 pm
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Mass spectrometry is a powerful tool for analyzing intact proteins. This seminar will focus on recommendations and practical considerations for success. Which instruments should you use? How much sample is required? What buffer components can be tolerated? Which modifications can be detected? How is the data analyzed? We will answer these questions and cover details of the ESI-LC/MS methods used at SUMS for intact protein MW determination.
Thursday April 2, 2020 - SUMS Seminar Series
Fundamentals: Measuring concentrations of small molecules using mass spectrometry - theory and practice, Part I
Karolina Krasinska, MS
Zoom webinar, noon-1 pm
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How can I measure concentrations of specific molecules in my sample? Can I use a mass spectrometer to analyze my samples of interest? What mass spectrometers are best suited for this purpose? What are the possible approaches and how do I determine which one is best for my application? What do I need to consider when planning such a project? This seminar will answer these questions and more, explaining mass spectrometry-based targeted quantitation from the ground up. Learn about common pitfalls and strategies to navigate around them. Gain practical tips on data analysis and what your data can and can’t tell you. Bring your questions, learn from your fellow researchers’ questions, and come away with a solid grounding in this core analytical technique.
Thursday March 26, 2020 - SUMS Seminar Series
Fundamentals: Quantitation strategies in mass spectrometry-based proteomics
Fang Liu, PhD
Zoom webinar, noon-1 pm
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This seminar will cover the most commonly used methods for mass spectrometry‐based quantification in proteomic applications. Quantification can be performed using either unlabeled or labeled approaches. Advantages and disadvantages, including quantification accuracy and reproducibility, will be discussed for each type of approach. This is a great opportunity for scientists who are new to mass spectrometry to learn about options available in qualitative and quantitative proteomics, and which method to choose for their research applications.
Sponsor: PharmaFluidics
Event Archive
Thursday April 14, 2022 - SUMS Seminar Series
Discovering the topology of protein complexes in situ using structural proteomics
Francis O'Reilly, PhD - Berlin Institute of Technology
Zoom webinar, noon-1 pm
Identifying the components and topologies of labile protein complexes in their native environments remains a major challenge in structural biology. Crosslinking mass spectrometry can identify residues that are nearby in space and is routinely used to study the structure of protein complexes in vitro. We have developed this technology towards mapping the topologies of protein complexes inside intact cells. I will show that the powerful combination of in-cell cross-linking mass spectrometry and cryo-electron tomography can expand our understanding of even ‘well-characterised’ protein complexes. We demonstrate this by describing the in situ architecture of a novel complex between a bacterial RNA polymerase and ribosome bridged through NusA, an anti-termination factor ubiquitous in bacteria.
Thursday March 12, 2020 - SUMS Seminar Series
Analyzing the volatilome via Secondary Electro-Spray Ionization (SESI): Technical development and its application to breath and microbial VOCs
Dr. Guillermo Vidal-de-Miguel, CEO, Fossil Ion Technology
Prof. Jiangjiang Zhu, Ohio State University
Thursday Free Lunch Seminar, noon-1 pm
Bass Biology 122
Sponsor: Diagnose Early Inc.
The metabolome is very dynamic, with many molecules being continuously absorbed, synthesized, and degraded in response to the environment and other endogenous stimuli. Its volatile fraction (the volatilome) is available non-invasively, but relevant metabolites tend to be very diluted. Secondary Electro-Spray Ionization (SESI) enables the real-time analysis of biologically relevant metabolites with very low vapor pressures at minute concentrations. This enabled applications like breath analysis for biomarker discovery, pharmacokinetic profiling, and micro-organism monitoring. This presentation will be divided into two: the technical development of SESI and its application to breath analysis, and the detection and monitoring of microbial VOCs for human health studies. A Super SESI instrument will be available in the laboratory for demonstration.
Thursday February 27, 2020 - SUMS Seminar Series
Capillary Electrophoresis coupled to Mass Spectrometry: Is the combination of exceptional speed, resolution and identification the holy grail of molecule characterization and monitoring?
Bill McCrea, MS
Thursday Free Lunch Seminar, noon-1 pm
Bass Biology 122
Capillary electrophoresis has been a trusted and highly valued technology for many years due to the exceptional speed and resolution of the separations. Unfortunately, the electrolytes and additives that make it so effective have traditionally limited CE to optical detection methods requiring additional analyses to determine absolute identification. The development of microfluidic ZipChip technology has resulted in highly efficient separations of both large and small molecules using ESI compatible background electrolytes. The combination of high-resolution CE separations and high-resolution mass spectrometric detection provides absolute identification with extremely fast runtimes for a variety of molecules in a wide range of matrices. Add into the equation nano-scale flow rates and nanoliter sample consumption -- is this the holy grail of analytical workflows?
Bill McCrea received his MS in Synthetic Chemistry from Montana State University and spent over 15 years in the biotech and pharmaceutical industries developing oncology drugs. During this time, It became clear that advanced technologies and instrumentation were the secret to improved efficiencies and getting more effective drugs to humans faster. Helping researchers on the front line of drug research, discovery and development get the most useful tools to overcome challenges and impact their research has become an obsession.
Sponsor: 908 Devices
February 19, 2020 - SUMS Seminar Series
High Resolution Ion Mobility Spectrometry and IMSn from Monosaccharides to Protein Complexes
Andy Baker, PhD
Wednesday Free Lunch Seminar, noon-1 pm
Bass Biology 121
Over the past two decades ion mobility (IM) coupled with mass spectrometry (MS) has evolved into an enabling analytical technique widely utilized in research areas ranging from small molecule structural elucidation to the detailed analysis of large protein complexes. A novel circular mobility separator allows scalable pathlength and enables very high (500+) resolution IMS experiments. In addition to the high mobility resolution, a number of novel experiments, including pre- and post mobility- fragmentation and IMSn experiments can be used to investigate ion structures. Selected examples of these experiments will be presented using model systems including nucleotides, sugars, proteins and small molecule imaging.
Andy Baker received his Ph.D in Analytical Chemistry from Indiana University working with Milos Novotny at the interface between problems of biochemical significance, high resolution chromatographic techniques, and mass spectrometric techniques. He is currently a Consulting MS Applications Scientist at Waters focusing on LC/MS/MS and LC/IMS/MS techniques for the characterization of target components from complex mixtures in both targeted and untargeted (‘OMIC) workflows.
Sponsor: Waters
January 22, 2020 - SUMS Seminar Series
LC/MS Analysis with Protein Metrics - The Basic, Best Practices, and Tips-n-Tricks
Speakers: Claire Bramwell, PhD; Maria Basanta-Sanchez, PhD; Marshall Bern, PhD; Eric Carlson, PhD
Wednesday Free Lunch Seminar, noon-1 pm
Bass Biology 121
Does your research rely on LC/MS analysis? Do you spend long hours on data analysis? Protein Metrics offers a broad set of solutions for post-data acquisition analysis covering a wide range of use cases and workflows. Come learn about various basics and some best practices for your proteomics MS/MS searches, analyses of cross-linking, detailed PTMs, ways of doing reporting, or simply some Tips-N-Tricks. Bring your data and we'll spend some time answering questions and helping you learn how to analyze your data better.
Sponsor: Protein Metrics
December 11, 2019 - SUMS Seminar Series
Mass Spec Fundamentals: what you didn’t know you needed to know
Speaker: Ryan Leib, PhD
Wednesday Free Lunch Seminar, noon-1 pm
Bass Biology 121
This seminar will cover the basic foundations of ion generation, manipulation, and detection in a typical LC/MS experiment, and why it matters to your research. This is a great jumping on point for scientists new to mass spectrometry who are excited to learn a bit about the underlying physical processes that make these experiments possible.
This is the first in a series of Fundamentals seminars; future presentations will cover other critical topics like experimental design, data analysis, and statistical modeling approaches to mass spectrometry results.
Sponsor: ThermoFisher Scientific
November 13, 2019 - SUMS Seminar Series
SpatialOMx offers highest cellular sensitivity and specificity for molecular analysis of tissue
Shannon Cornett, PhD - Imaging/MRMS Applications Manager, Bruker Daltonics
Wednesday Free Lunch Seminar, noon-1 pm
Bass Biology 121
Abstract: LC-MS analyses of tissue homogenates identify a wide range of compounds extracted from all cell phenotypes in the homogenate. Often, however, signals originating from discrete cells cannot be distinguished from signals from other cell phenotypes in the tissue. MALDI Imaging is a molecular mapping tool which captures molecular signals directly from tissue and has been shown to differentiate cell phenotype even when histological analysis is indeterminate. Combined, the two techniques enable a SpatialOMx approach to studying molecular changes in tissue. Learn how timsTOF fleX with its dual ESI/MALDI ion source powers MALDI guided SpatialOMx to offer the most specific molecular insight into cellular processes.
Sponsor: Bruker
October 30, 2019 - SUMS Seminar Series
Atmospheric Ion Mobility Spectrometry - Applications for Macromolecular Analysis
Dr. Henry Benner - CEO, IonDx
Wednesday Free Lunch Seminar, noon-1 pm
Bass Biology 121
Abstract: Regulatory agencies require biotech organizations to perform detailed structural analysis of their biotherapeutics. This involves primary, secondary, tertiary and quaternary structural assessment. The majority of higher order structural analytics rely on indirect biophysical techniques because x-ray crystallography is not easily implemented in biotherapeutic workflows. A well-recognized technical challenge is to screen and fingerprint protein structures more rapidly. In this seminar we will provide background information on atmospheric pressure ion mobility spectrometry (IMS), an emerging analytical technology attempting to address this concern. We will showcase historical applications as well as recent research work on various classes of proteins, including monoclonal antibodies. We hope that this scientific webinar will introduce the audience to IMS and provide a forum for discussing potential applications for studying various protein-protein interactions, protein-nucleic acid structures and other exciting modalities.
Sponsor: IonDX