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
• Targeting and quantifying small molecules 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.