Mass Spec Fundamentals Seminars
Proteomic Workshop
Craig Dufresne, PhD - Staff Scientist, Thermo Fisher Scientific
Steven Danielson, PhD - LCMS Technical Specialist, Thermo Fisher Scientific
Day 1 Tuesday, February 13th 2024
10:00 am – 12:00 pm
Identifying Quantitative Protein Changes in Iris Biopsies of Glaucoma Patients Using Label Free Quantitative Proteomics from High Resolution Orbitrap
Presenter: Dr. Craig Dufresne
12:00-1:00 pm: Lunch provided by Thermo
1:00- 2:00 pm
Sample Preparation Techniques for Proteomics or Targeted Peptide Quantification
Presenter: Dr. Craig Dufresne
2:00-3:00 pm
Introduction to the Types of MS Systems and Their Data
Presenter: Dr. Steven Danielson
See .pdf of slides
Day 2 February 14th 2024
9:00 AM start time, end around 4:00 pm
Hands on Training for Data Dependent Orbitrap Mass Spectrometry
Presenter: Dr. Craig Dufresne
Day 3 February 15th 2024
9:00 AM start time, end around 4:00 pm
Proteome Discoverer: A Hands-on Approach
Presenter: Dr. Craig Dufresne
Fundamentals: An introduction to MS-based glycoproteomics
Nick Riley, PhD - Dept. of Chemistry, Stanford University
Zoom webinar, noon-1 pm
View recorded webinar
Download .pdf of slides
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
View recorded webinar
Download .pdf of slides
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.
Thursday July 2, 2020 - SUMS Seminar Series
Fundamentals: Bioanalytical LC/MS method validation -- fit for purpose
Ludmila Alexandrova, PhD
Zoom webinar, noon-1 pm
View recorded webinar
Download .pdf of slides
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 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
View recorded webinar
Download .pdf of slides
Thursday May 7, 2020 - SUMS Seminar Series
Fundamentals: Native mass spectrometry & relevant techniques
Beryl Xia, PhD
Zoom webinar, noon-1 pm
View recorded webinar
Download .pdf of slides
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
View recorded webinar
Download .pdf of slides
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
View recorded webinar
Download .pdf of slides
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
View recorded webinar
Download .pdf of slides
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
View recorded webinar
Download .pdf of slides
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
View recorded webinar
Download .pdf of slides
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
View recorded webinar
Download .pdf of slides
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