Sunday, March 7, 2010, 9:00 am - 4:00 pm (with one hour break for lunch-on-your-own)

Instructors:  Susan Abbatiello (Broad Institute), Michael MacCoss (University of Washington), Brendan MacLean (University of Washington), and Gary Valaskovic (New Objective)

Course Description

Modern tandem mass spectrometers combined with database searching software have made the qualitative analysis of complex peptide mixtures fairly routine, however, the accurate and precise detection of differences in peptide abundance remains a considerably greater challenge. While a broad range of methods for quantitative proteomics are being developed for both targeted and discovery proteomics, the application of these methods are not nearly as robust as those used for peptide identification.  The technical details associated with study design, sample preparation, nanoflow liquid chromatography, electrospray stability, run order, etc... have much greater effects in the context of a quantitative experiment.  Furthermore, while there are now numerous commercial and free database searching tools that have been improved and thoroughly vetted by the community over the last decade, the equivalent computational tools that are vendor neutral and robust do not exist for quantitative analysis of these data. 

 

This course will focus on the fundamentals necessary to perform quantitative proteomics experiments.  Emphasis will be placed on the basics of study design, quality control, and validation as opposed to being comprehensive in the description of approaches used by the community.  Examples of troubles and challenges in performing these experiments will be chosen from the instructors' personal experience.  The course will be interactive requiring active attendee participation with breakout problem solving sessions and live software demonstrations.

 

Tuition:  $150