Course Schedule

2019 UW Course

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.