Proteomics Mass Spectrometry Data Analysis

Introduction to common techniques for the analysis and quantitation of proteomics mass spectrometry ("mass spec") data.  Topics covered will include the concept of Peptide-Spectra Matching (PSM) versus de novo sequencing, as well as the application of commonly used algorithms such as Andromeda (Maxquant), Comet (Sequest), and Mascot.  Key parameters for different search engines will be discussed along with the statistical significance of their respective outputs.  Statistics for these data types - and how quantitation can be done for different experimental setups - will be discussed in the context of the Skyline application.  The first day will be primarily lecture-driven while the second will focus on hands-on analysis of data