Skyline Course Schedule Buck Institute 4/2 - 4/6 2018

 Introduction to targeted quantitative proteomics and Skyline

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

Posttranslational modifications, MS1 and targeting DDA data

  • Posttranslational modifications – specific challenges
  • PRM assays
  • MS1 Filtering
  • Tutorial: SRM libraries and iRT
  • Small molecules

Computational methods, statistics for quantitative experiments and Panorama

  • Statistical considerations in study design
  • Statistical analysis of proteomics experiments
  • Data reports
  • System suitability and quality control
  • Tutorial: Sharing and publishing Skyline processed data in Panorama

DIA, methods and integrated data analysis

  • Introduction data independent acquisition (DIA)
  • Skyline peak picking algorithms, FDR rates, high throughput pipeline
  • Tutorial: Analysis of DIA data in Skyline
  • DIA FDR rates, automatic interference filter
  • DIA high throughput and comprehensive quantification for biological datasets
Additional DIA and industry applications, targeted experiments and the future
  • Keynote Lecture by Buck Institute Faculty – Aging Research and Mass Spectrometry
  • DIA applications and discussions
  • Combining different scan-types and workflows (MS1 Filtering, SRM, PRM, DIA)
  • Tutorial: Processing grouped study data in Skyline
  • Review and test
  • Skyline and Industry applications
  • Conclusion:  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.