Course Schedule


Monday: Introduction to Translational Mass Spectrometry and Skyline 

  • Welcome and introduction to translational mass spectrometry
  • Introduction to Skyline
  • Tutorial: MS1 based differential expression in Skyline
  • Tutorial: Processing grouped study data in Skyline
  • Basics of mass spectrometry for targeted MS

Tuesday: Targeted proteomics, MRM and PRM (Parallel Reaction Monitoring)

  • Intro to targeted proteomics and quantitative analysis
  • Tutorial: SRM method development and refinement
  • Peptide selection for targeted proteomics
  • PRM method development
  • Tutorial: Working with PRM data

Wednesday: System Suitability, Standards, and Absolute Quantification

  • Publishing data using Panorama
  • System suitability and quality control in Skyline and AutoQC
  • Standards for targeted proteomics
  • Tutorial: Signal calibration and absolute quantification (peptides and proteins)
  • Quantification of clinical biomarkers

Thursday: Quantification of Small Molecules Using Skyline, Ion Mobility

  • Introduction to small molecule capabilities in Skyline
  • Tutorial: Small molecule method development using Skyline
  • Tutorial: Analysis of high resolution metabolomics data in Skyline
  • Targeted analysis of ion mobility dData
  • Tutorial (IMS in Skyline)

Friday: Data Independent Analysis, PTM Localization, and Targeted Discovery

  • Introduction to data independent acquisition (DIA)
  • Tutorial: Analysis of DIA data in Skyline
  • PTM localization in Skyline
  • The advent of “Targeted Discovery” using large targeted panels
  • Feedback and close of meeting