CSHL Course on Proteomics (2025-2029)

Cold Spring Harbor Laboratory, Cold Spg Hbr NY

Investigators

Abstract

Abstract CSHL Proteomics Course The proposed Cold Spring Harbor Laboratory Course on Proteomics is to be held each summer from 2025 through 2029. 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, proteomics is an enabling core technology to probe biological activities in parallel, providing unprecedented analytical insight 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 be trained in experimental design and sample preparation, they will acquire high-sensitivity liquid chromatography tandem mass spectrometry (LC-MS/MS) data, and will be taught how to reliably interpret this data at both the level of identification and quantification. Students will gain practical experience in analysis of intact proteins, purifying and identifying protein- protein interactions through proximity-based biotinylation or resulting from direct chemical cross-linking; and enriching/characterizing post-translationally modified peptides using the latest methods. Students will gain hands-on experience in quantitative proteomic analysis methods: they will be taught label-free and covalent isotopic-labeling approaches to differentially profile changes in proteomes. Students will be trained to select and design transitions for targeted peptides and to setup and perform parallel reaction monitoring mass spectrometry assays to accurately quantify proteins of most interest. They will also learn how to analyze data-independent acquisition (DIA) data, where broad mass range tandem mass spectrometry data acquisition allows surveying of all components in a sample. They will get hands-on experience in de novo interpretation of mass spectrometry data prior to being trained in database searching software to give a better understanding of the underlying data. For all sections of the course, a strong emphasis will be placed on data analysis, understanding the reliability of results, and learning how to convert this data into biological insight. Lecturers will include people from academia, reagent developers and people working in the pharmaceutical industry, providing a range of perspectives of the field of proteomics. The overall aim of the course is to provide each student with the fundamental knowledge and hands-on experience necessary to be able to design, perform and properly analyze proteomic experiments. The long-term goal is to train students to identify new opportunities and applications for proteomics approaches in their biological research and to learn how to integrate these into systems biology and model organism approaches to human biology and health.