S4 - Advanced Proteomics Topics

2022-10 Skyline Online


This course schedule will address mass spectrometry approaches for advanced quantitative proteomics including data independent acquisition (DIA) and post translational modifications (PTM), with topics spanning instrument method design and setup for DIA, processing DIA data within Skyline, special considerations for targeted quantification of PTMs, and, of course, learning to use Skyline software more effectively in your research. The instructor list includes researchers from both academia and industry with a wealth of combined experience in targeted and quantitative proteomics, and using Skyline to meet the needs of diverse research questions.

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 Introduction to Skyline course.

Instructors: Lindsay Pino, Juan Rojas, Weixian Deng, Natan Basisty, Deanna Plubell


Day 1 - Thursday, October 20, 2022 
9:00 am - 5:00 pm (All times EST)

  • 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, October 21, 2022 
9:00 am - 5:00 pm (All times EST)

  • 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