Monday: Introduction to targeted quantitative proteomics and Skyline
- Meet at Foege S. (between Foege South and North) at 9am
- Welcome and intro to targeted proteomics and quantitative analysis
- Basics of mass spectrometry for targeted MS
- Intro to Skyline
- Tutorial: SRM method development and refinement
Tuesday: Panorama, parallel reaction monitoring, system suitability and iRT
- PRM method development
- Tutorial: Working with PRM data
- System suitability and quality control
- Tutorial: Using Panorama for publishing data and Auto QC
- Tutorial: SRM libraries and iRT
Wednesday: Standards, calibration, statistics for quantitative experiments and Panorama
- Statistical considerations in study design
- Statistical analysis of proteomics experiments
- Standards for targeted proteomics
- Signal calibration and absolute quantification
- Tutorial: Targeting DDA data with MS1 filtering in Skyline
Thursday: Sample prep, DIA, methods and data analysis
- Sample prep for targeted proteomics
- Introduction data independent acquisition (DIA)
- Tutorial: Analysis of DIA data in Skyline
Friday: Plasma proteomics and the future
- Plasma proteomics - Validation
- Tutorial: Processing grouped study data in Skyline
- Review and test
- Conclusion: The future of targeted proteomics
The course also includes popular morning “Sky-Jam” sessions led by Brendan MacLean with hands-on Skyline processing.
Note: As instructors update their content for this course, this list may change slightly.