Abstract CSHL Proteomics Course The proposed Cold Spring Harbor Laboratory Course on Proteomics is to be held each summer from 2018 through 2022. Proteomics is one of the pillar technologies of systems biology by which hundreds or thousands of proteins can be monitored and characterized simultaneously. In combination with genomics and metabolomics approaches, proteomics is an enabling core technology to probe biological activities in parallel, providing unprecedented analytical power into diverse biological processes in mammalian development and disease. Models of many human diseases have been developed in a wide variety of animal systems, in particular vertebrate models such as mouse, zebrafish, rat and frog, and invertebrate models such as worms and flies; and increasingly the use of new stem cell technologies is being harnessed to produce powerful in vitro models to be deployed alongside animal models. There is a growing need for implementation of systems biology approaches to these models, which necessitates an in-depth understanding of the challenges and pitfalls of various “high-throughput” technologies, achieved in part by hands-on and highly focused training. This intensive two week laboratory and lecture course will focus on cutting-edge proteomics approaches and technologies. Students will gain practical experience purifying and identifying protein complexes and enriching/characterizing post-translationally modified peptides using the latest methods. In the protein profiling portion of the course, students will gain hands-on experience in quantitative proteome analysis methods: they will be taught label-free and covalent isotopic-labeling approaches to differentially profile changes in proteomes. Students will be trained in high-sensitivity, microcapillary high pressure liquid chromatography (nanoHPLC) coupled with nanospray-ESI and tandem mass spectrometry. Both single dimension and multidimensional separation methods coupled to mass spectrometry will be taught. In the targeted proteomics section of the course, students will be taught to analyze and process shotgun proteomics data in order to accurately identify and quantify selected proteins: they will be trained to select and design transitions for targeted peptides and to setup and perform SRM/MRM mass spectrometry assays. They will learn to process and interpret the acquired data to measure and validate changing quantities of targeted proteins in a variety of biological samples. For all sections of the course, a strong emphasis will be placed on data analysis. Outside lecturers will discuss proteomics topics and methods not directly covered in the course including de novo sequence analysis; 2D-gel fractionations and detecting/quantifying protein-level changes using DIGE; advanced mass spectrometry methods; statistics; the analysis of intact proteins, and native mass spectrometry; and functional proteomics. The overall aim of the course is to provide each student with the fundame...