Buck Institute Targeted Proteomics Course - Buck Institute April 13 - 17, 2020

 Introduction to targeted quantitative proteomics and Skyline

  • Meet at Buck Institute at 9 am
  • Welcome and intro to quantitative analysis
  • Basics of mass spectrometry and SRM
  • From discovery to targeted proteomics
  • Intro to Skyline
  • Tutorial: SRM method development
  • From discovery to targeted quantification

PRM and quantification

  • Introduction to iRT
  • Tutorial: iRT
  • Absolute quantification adn calibration curves
  • Tutorials: Manual data analysis and grouped studies
  • PRM method development
  • Hands-on: PRM data analysis

Computational methods, statistics for quantitative experiments and Panorama

  • Statistical considerations in study design
  • MSstats and its integration with Skyline
  • Tutorials: Using MSstats R package for analysis and applications
  • Data Independent Acquisition (DIA) - cross lab study and new advances
  • Statistical analysis of proteomics experiments
  • Intro to Panorama 
  • Panorama autoQC, calibration curves and reporting

DIA, methods and integrated data analysis

  • Biomarker Studies - design and applications
  • Skyline processing of DDA data (MS1 filtering) 
  • Intro to DIA
  • Tutorial: Analysis of DIA data in Skyline
Small molecule research and the future of targeted experiments
  • Small molecule applications 
  • Tutorial: Small molecule research in Skyline
  • Small molecule iomers
  • Skyline and industry applications
  • The future of targeted proteomics

The course includes voluntary but very popular morning (8am!) "Sky-Jam" sessions led by Brendan MacLean with hands-on Skyline processing.