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 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.