Monday: Introduction to targeted quantitative proteomics and Skyline

• Meet at Foege S. (between Foege South and North) 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, immuno-enrichment, system suitability and targeting DDA data

• Plasma proteomics
• Immuno-SRM and SISCAPA
• System suitability and quality control
• Tutorial: Targeting DDA data with MS1 filtering in Skyline

Wednesday: Standards, calibration, statistics for quantitative experiments and Panorama

• Standards for targeted proteomics
• Signal calibration and absolute quantification
• Statistical considerations in study design
• Statistical analysis of proteomics experiments
• Tutorial: Processing grouped study data in Skyline
• Tutorial: Sharing and publishing Skyline processed data in Panorama

Thursday: Sample prep, DIA, methods and data analysis

• Sample prep for targeted proteomics
• Introduction data independent acquisition (DIA)
• Setting up targeted methods at the instrument
• Tutorial: Analysis of DIA data in Skyline

Friday: nanoLC, troubleshooting and the future

• nanoLC for proteomics
• System troubleshooting for best results
• Conclusion:  The future of targeted proteomics
• End at 2:30pm