# Cold Spring Harbor Laboratory Course on Proteomics

> **NIH NIH R25** · COLD SPRING HARBOR LABORATORY · 2021 · $123,254

## Abstract

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...

## Key facts

- **NIH application ID:** 10160648
- **Project number:** 5R25HD072999-09
- **Recipient organization:** COLD SPRING HARBOR LABORATORY
- **Principal Investigator:** DAVID J. STEWART
- **Activity code:** R25 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $123,254
- **Award type:** 5
- **Project period:** 2018-08-03 → 2023-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10160648

## Citation

> US National Institutes of Health, RePORTER application 10160648, Cold Spring Harbor Laboratory Course on Proteomics (5R25HD072999-09). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10160648. Licensed CC0.

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