Daojing Wang, PhD - Founder & CEO, Newomics Inc.
In person and online:
Bass Biology conference room 122 / Zoom webinar, noon-1 pm
Lunch provided by Newomics
View recordingProteomics 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.
Daniel Hornburg - Senior Director, Discovery, Research and Tech Development, Seer Inc.
In person and online:
Bass Biology conference room 102 / Zoom webinar, noon-1 pm
Lunch provided by Seer
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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.
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.
Norah Brown, MS - Stanford University
In person and online:
Bass Biology conference room 122 / Zoom webinar, noon-1 pm
Lunch provided by Promega
View recordingProteomics 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.
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.
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.
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.
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 spectrometery who are excited to learn a bit about the underlying physical processes that make these experiments possible.
Momei Zhou, PhD - Dept. of Pediatrics, Stanford University School of Medicine
Zoom webinar, noon-1 pm
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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.
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.
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
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.
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.
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:
Zoom meeting, noon-1 pm
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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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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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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.
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.
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.
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.
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.
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.
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
Francis O'Reilly, PhD - Berlin Institute of Technology
Zoom webinar, noon-1 pmIdentifying 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.
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.
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
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
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
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 spectrometery 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
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
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