Events

Webinars Available On-Demand

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.

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 spectrometery who are excited to learn a bit about the underlying physical processes that make these experiments possible.

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.

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

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.

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.

Seminar series is on hiatus during the online ASMS Reboot

https://asms.org/conferences/asms-2020-reboot/

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:

Zoom meeting, noon-1 pm
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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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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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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.

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.

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.

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.

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.

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.

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