Description:
This course schedule will address mass spectrometry approaches for advanced quantitative proteomics including data independent acquisition (DIA) and post translational modifications (PTM), with topics spanning instrument method design and setup for DIA, processing DIA data, special considerations for targeted quantification of PTMs, and, of course, learning to use Skyline software more effectively in your research. The instructor list includes researchers from both academia and industry with a wealth of combined experience in targeted and quantitative proteomics, and using Skyline to meet the needs of diverse research questions.
This course assumes students will have a basic working knowledge of the Skyline software and how to use it, either through experience or by attending the Intro to Skyline course.
Instructors: TBD
Schedule:
Day 1 - Thursday, October 16, 2025
11:00am - 7:00pm (All times EST)
- Introduction to data independent acquisition (DIA)
- DIA instrument setup
- Generating DIA-only libraries with EncyclopeDIA
- Analysis and manual curation of DIA data
- IMS filtering for diaPASEF
Day 2 - Friday, October 17, 2025
11:00am - 7:00pm (All times EST)
- Introduction to post translational modifications (PTMs)
- PTM data walkthrough, Skyline tips and tricks for PTM quantification
- Introduction to high throughput mass spectrometry proteomics
- Advanced process control and analysis considerations for big data
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