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The course will start on Monday at 8:45 am and finish on Friday at 6:00 pm.

Day 1: Biological significance and introduction to SWATH/DIA

  • Welcome
  • Opening Lecture: Biological significance of SWATH-MS experiments (Ruedi Aebersold)
  • Lecture: Targeted Proteomics Primer (Christina Ludwig)
  • Lecture: Quality control in MS-based proteomics (Eduard Sabido)
  • Lecture: Introduction to DIA/SWATH acquisition and concepts (Ben Collins)
  • Lecture: Generating Libraries for DIA/SWATH analysis (Ben Collins)
  • Tutorial: Library Generation from DDA files
  • Lecture: General principles of quantitative proteomics (Christina Ludwig)

Day 2: Concepts of peptide-centric analysis

  • Lecture: Introduction to DIA on orbitraps and peptide-centric versus spectrum-centric analysis (Michael MacCoss)
  • Lecture: mProphet - Automated peak picking and false discovery rates (Ludovic Gillet)
  • Lecture: Details on FDR control in DIA workflows and related workflows (Isabel Bludau)
  • Lecture: Introduction to Skyline for DIA analysis (Brendan MacLean)
  • Tutorial: Skyline set up for DIA
  • Tutorial: Skyline DIA analysis

Day 3: Concepts of spectrum-centric analysis

  • Lecture: Introduction to spectrum-centric analysis of DIA data (Alexey Nesvizhskii)
  • Lecture: Introduction to experimental design and statistical analysis (Olga Vitek)
  • Lecture: DIA-UMPIRE (Alexey Nesvizhskii)
  • Tutorial: DIA-UMPIRE
  • SkyJam: Advanced analysis of DIA data with Skyline (Brendan MacLean)

Day 4: Data analysis in comparison

  • Keynote: Recent developments and future direction in DIA (Michael MacCoss)
  • Tutorial: OpenSWATH, pyprophet and TRIC
  • Lecture: Analysis of post-translational modifications by SWATH-MS (Ariel Bensimon)
  • Keynote: Statistical analysis of DIA data (Olga Vitek)

Day 5: Downstream analysis of DIA/SWATH data

  • Lecture: An industrial perspective on DIA and the Spectronaut software (Lukas Reiter)
  • Tutorial: Statistics
  • Keynote: Biological applications of SWATH-MS (Ruedi Aebersold)
  • Summary - Wrap up - Discussions