S2 - Advanced Small Molecule Topics

2022-10 Skyline Online


While originally developed for targeted proteomics applications, Skyline is now a rapidly evolving tool for method development and data analysis of small molecule mass spectrometry data. Skyline supports workflows including MRM, PRM, and high-resolution DDA, DIA, and IMS-MS measurement of virtually any molecule. In this course, users will learn how to expand their Skyline horizons beyond those of amino-acid based peptides, to include virtually any molecule. The course will include but not necessarily be limited to the following topics: setting up new methods from transition lists and spectral libraries, building and evaluating metabolomics system suitability tests, performing collision energy and method optimization, mining high-resolution metabolomics data, ion mobility MS of lipids and building spectral libraries, retention time normalization, and multiplexed calibrated quantitative methods.

This course assumes students will have a basic working knowledge of the Skyline software and how to use it, either through experience or by attending the Intro to Skyline course.

Instructors: Chris Ashwood, Erin Baker, Kaylie Kirkwood, Michael Davern


Day 1 - Thursday, October 13, 2022 
9am - 5:00 pm (All times EST)

  • Advanced methods for small molecule research in Skyline
  • Small molecule method development
  • System suitability for small molecules
  • Advanced small molecule quantification (multiplexed panels)
  • Analysis of high resolution metabolomics data

Day 2 - Friday, October 14, 2022 
9am - 5:00 pm (All times EST)

  • Ion mobility in proteomics and metabolomics
  • Analysis of lipidomics data in Skyline
  • Retention time normalization
  • The future of small molecule analysis in Skyline