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Mass Spec Fundamentals Seminars

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February 13-15, 2024

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

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
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 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.