S1 - Introduction to Skyline

2022-10 Skyline Online


This course will address a range of targeted techniques using selected reaction monitoring (SRM) and parallel reaction monitoring (PRM) mass spectrometry approaches for targeted quantitative proteomics and other small molecule -omics. Session topics will include an introduction to setting up target lists for peptides and small molecules, basic importing and understanding targeted mass spectrometer data, absolute quantification, differential abundance testing, and a general focus on learning to use Skyline software effectively in your research. The instructor list includes researchers and the Skyline project lead, all with a wealth of combined experience in targeted and quantitative mass spectrometry, and both using and creating Skyline to meet the needs of diverse research questions.

Instructors: Brendan MacLean, Chris Ashwood, Ruth Huttenhain, Lilian Heil, and Juan Rojas.


Day 1 - Monday, October 10, 2022 
9:00 am - 5:00 pm (All times EST)

  • Introduction to targeted proteomics in Skyline
  • The Skyline software ecosystem
  • Targeted MS/MS (PRM) with peptides
  • Absolute quantification and calibration curves for peptides

Day 2 - Tuesday, October 11, 2022 
9:00 am - 5:00 pm (All times EST)

  • Grouped study data processing
  • Intro to small molecule research in Skyline
  • Small molecule targets
  • Small molecule quantification