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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: tbd (Ruedi Aebersold)
  • Lecture: Introduction to DIA/SWATH acquisition and concepts (Ben Collins)
  • Lecture: Introduction to experimental design and statistical analysis (Olga Vitek)
  • Lecture: Generating Libraries for DIA/SWATH analysis (Ben Collins)
  • Tutorial: Library Generation from DDA files

Day 2: Concepts of peptide-centric analysis

  • Lecture: Introduction to peptide-centric analysis and DIA on trapping instruments (Michael MacCoss)
  • Lecture: Concepts of peptide-centric DIA data analysis & mProphet (Ludovic Gillet)
  • Lecture: FDR control in the DIA workflow and TRIC alignment (Isabell Bludau)
  • Lecture: Introduction to Skyline for DIA analysis (Brendan MacLean)
  • Tutorial: Skyline set up for DIA
  • Tutorial: Skyline DIA analysis
  • Lecture: Skyline DIA examples (Brendan MacLean)
  • Lecture: Acquisition methods on Q-TOF and Q-Orbitrap (Ludovic Gillet)

Day 3: Spectrum-centric analysis, quantification and statistics

  • Keynote: Introduction to spectrum-centric analysis of DIA data (Alexey Nesvizhskii)
  • Lecture: Using DIA-Umpire and related tools (Alexey Nesvizhskii)
  • Tutorial: DIA-UMPIRE
  • Keynote: Statistical analysis of DIA data (Olga Vitek)
  • Lecture: Qunatification concepts and label free quantification (Christina Ludwig)

Day 4: Hands on analysis and future developments

  • Keynote: Future developments in DIA (Michael MacCoss)
  • Tutorial: OpenSWATH, pyprophet and TRIC
  • Tutorial: Statistical analysis using MSstats
  • Skyline Session: Visualizing external data in Skyline (Brendan MacLean)
  • Skyline Session: tbd (Brendan MacLean)

Day 5: Post-translational modifications and DIA applications

  • Lecture: Concepts of PTM analysis using DIA (Christina Ludwig)
  • Lecture: Inference of peptidoforms (IPF) (George Rosenberger)
  • Tutorial: PTM analysis using IPF
  • Lecture: Tiered iRT: Making best use of multiple RT spaces for DIA (Lukas Reiter)
  • Closing Lecture: tbd (Ruedi Aebersold)
  • Summary - Wrap up - Discussions

The regular program will be accompanied by Morning-SkyJams.