Session 1 - Introduction to Skyline for Targeting Peptides and Small Molecules: SRM/MRM and PRM

• 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 - Tueday, April 13, 2021 
9am - 5:00 pm (All times EDT)

Session 2 - Advanced Topics in Skyline for Small Molecules

• Skyline for small molecules
• Method transfer and quantification
• System suitability for small molecules
• Advanced small molecule quantification (multiplexed panels)
• Analysis of high resolution metabolomics data

Day 2 - Friday, April 16, 2021
9:00 am - 5:00 pm (All times EDT)

• Ion mobility in proteomics and metabolomics (iRT)
• Analysis of lipidomics data in Skyline
• Isotope incorporation / flux analysis in Skyline
• Gas chromatography-mass spectrometry analysis
• The future of small molecule analysis in Skyline

Session 3 - Introduction to Targeted Proteomics: SRM/MRM and PRM

Day 1 - Monday April 19, 2021
9am - 5:00 pm (All times EDT)

• Introduction to targeted proteomics in Skyline
• The Skyline ecosystem
• Targeted MS/MS (PRM)
• Small molecule method transfer and quantification
• Absolute quantification and calibration curves

Day 2 - Tuesday April 20, 2021
9am - 5:00 pm (All times EDT)

• Maual data analysis
• Using indexed retention time (iRT)
• Grouped study data processing in Skyline
• Using Panorama and AutoQC

Session 4 - Advanced Quantitative Proteomics: DIA and PTMs

Day 1 - Thursday April 22, 2021 
9am - 5:00 pm (All times EDT)

• Introduction to data independent acquisition (DIA)
• Analysis of DIA data in Skyline
• DIA instrument setup
• Generating DIA-only libraries with EncyclopeDIA
• IMS filtering for DDA and DIA quantitation

Day 2 - Friday April 23, 2021 
9am - 5:00 pm (All times EDT)

• Introduction to post transitional modifiers (PTMs)
• Carbonyl PTM walkthrough
• Skyline tips and tricks for PTM quantification
• Advanced process control for big data
• Open searching and DIA