Monday: Introduction to targeted quantitative proteomics and Skyline

  • Meet at Buck Institute at 9am
  • Welcome and intro to quantitative analysis
  • Basics of mass spectrometry for targeted MS
  • Intro to Skyline
  • Tutorial: SRM method development and refinement

Tuesday: Plasma, posttranslational modifications, system suitability and targeting DDA data

  • Plasma proteomics, high throughput SRM assays
  • Posttranslational modifications
  • MS1 Filtering and PRM assays
  • System suitability and quality control
  • Tutorial: SRM libraries and iRT

Wednesday: computational methods, statistics for quantitative experiments and Panorama

  • Statistical considerations in study design
  • Statistical analysis of proteomics experiments
  • Computational  methods in R and Skyline
  • Signal calibration and absolute quantification
  • Tutorial: Sharing and publishing Skyline processed data in Panorama

Thursday: DIA, methods and integrated data analysis

  • Introduction data independent acquisition (DIA)
  • Skyline peak picking algorithms, FDR rates, high though put pipeline
  • Tutorial: Analysis of DIA data in Skyline

Friday: nanoLC, targeted experiments and the future

  • nanoLC for proteomics
  • Tutorial: Processing grouped study data in Skyline
  • Review and test
  • Skyline and Industry applications
  • Conclusion:  The future of targeted proteomics

The course also includes popular morning “Sky-Jam” sessions led by Brendan MacLean with hands-on Skyline processing.