This 2.5 day short course will walk through the process of designing, developing, and statistically evaluating LC-MS methods for the targeted quantification of peptides with high confidence.  Topics covered will include peptide selection from target proteins, optimization of peptide transitions, LC gradient, collision energy, and discussion on internal standards.  Attendees will learn rigorous method evaluation and performance characterization, limits of detection and quantification calculation, and use of routine System Suitability QC.  Case studies and tutorials will be provided for hands-on participation with open-source software Skyline (

Target audience

    Target audience are experimental scientists with experience in proteomic research. We also welcome computational scientists interested in working with raw mass spectrometric data.


    • Sue Abbatiello, Andy Hoofnagle, Christina Ludwig, Lindsay Pino