Basics of targeted mass spectrometry with Skyline

I kicked off the scientific presentations for the virtualized Northeastern University May Institute with a workshop on the basics of mass spectrometry proteomics. In this mixed-methods 1.5 hour session, I aimed to give biomedical researchers a crash course in all things quantitative mass spectrometry-based proteomics and even give some of the pros a few tips on the Skyline software ecosystem. By the end of this workshop, I wanted participants to come away with the ability to:

  1. Assess the experimental pros and cons of targeted proteomics, and compare to discovery proteomics.
  2. Explain the fundamentals of mass spectrometry proteomics, including peptide fragmentation and basic components of a mass spectrometer
  3. Describe the steps of a targeted proteomics workflow and the information required to build an assay
  4. Apply the Skyline software ecosystem to their own targeted proteomics experiments.

Throughout the lecture-based workshop, I mixed participant question-and-answer and examples of the concepts discussed in Skyline. Finally, I closed with three hands-on examples of using Skyline to build a Parallel Reaction Monitoring (PRM) mass spectrometry experiment.

You can check out the recording below:

Author: Lindsay K Pino

Postdoctoral researcher in the Epigenetics Institute at University of Pennsylvania

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