Short Courses

The short course will discuss design and analysis of quantitative shotgun proteomic experiments with tandem mass tag (TMT) labeling. The course will first introduce the fundamental principles of statistical experimental design as applied to quantitative proteomic experiments with TMT labeling. We will then give an introduction to quantification workflows in the FragPipe computational pipeline, followed by a hands-on session with FragPipe. Next, we will discuss statistical models for relative protein quantification in the software MSstatsTMT, and give a hands-on tutorial on MSstatsTMT. Finally, the course will use case studies to illustrate the impact of various options within FragPipe on detection of differentially abundant proteins. Prior exposure to statistics and the R programming language is not required.

The short course will discuss design and analysis of quantitative shotgun proteomic experiments with tandem mass tag (TMT) labeling. The course will first introduce the fundamental principles of statistical experimental design as applied to quantitative proteomic experiments with TMT labeling. We will then give an introduction to quantification workflows in the FragPipe computational pipeline, followed by a hands-on session with FragPipe. Next, we will discuss statistical models for relative protein quantification in the software MSstatsTMT, and give a hands-on tutorial on MSstatsTMT. Finally, the course will use case studies to illustrate the impact of various options within FragPipe on detection of differentially abundant proteins. Prior exposure to statistics and the R programming language is not required.

1. Innovative Methods 
   1. Structural Glycomics for Precision Medicine, Rebekah Gundry
   2. Conformational Diagnostics by Mass Spectrometry, Johns Yates
   3. Acoustic Ejection Mass Spectrometry (AEMS) for Enabling Very Large Protein Biomarker Validation Studies, Christie Hunter
2. Clinical Domains for Biomarker
   1. AD and Aging: The Road to Circulating Biomarkers, Birgit Schilling
   2. Apolipoprotein and complex trait genetics in coronary artery disease (PROCARDIS)), Manuel Mayr
3. Making (hopefully) to the clinic
   1. Health Surveillance MRM Assay from Development to Getting Ready for CLIA, Esthelle Hoedt

Our understanding of how the biology of various diseases relates to the central dogma that DNA encodes RNA, which encodes protein has been buoyed by rapid technological advances in DNA and RNA sequencing and has led to some of the first advances in personalized medicine. However, characterization of the final and arguably most actionable element of the central dogma, protein, has lagged behind. Among the various proteomic parameters, a complete description of post-translational modifications (PTMs) in any given cell remains a daunting task. The entire repertoire of PTMs is vast (~400 different types). The modifications events are chemically diverse, and often are difficult to pinpoint with single amino acid resolution. Our current understanding of many types of PTMs, therefore, is fragmentary, where a substantial fraction has not been sampled and characterized within a physiological relevant setting. In this workshop, a number of world leaders will provide an overview of mass spectrometric analyses of protein PTMs that are involved in a wide variety of pathophysiological processes. The workshop will also provide practical steps on the proteomic experimental design (sample preparation, instrumentation and bioinformatics) as well as biological interpretation of the proteomic data.