Protocol

Quantitative Methods in Proteomics

Volume 893 of the series Methods in Molecular Biology pp 511-522

Date:

MSQuant: A Platform for Stable Isotope-Based Quantitative Proteomics

  • Joost W. GouwAffiliated withDepartment of Biochemistry and Molecular Biology, Centre for High-Throughput Biology, University of British Columbia
  • , Jeroen KrijgsveldAffiliated withGenome Biology Unit & Proteomics Core Facility, EMBL Email author 

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Abstract

Quantitative approaches in proteomics are emerging as a powerful tool to probe the dynamics of protein expression across biological conditions. Thereby, quantification helps to recognize proteins with potential biological relevance, which greatly aids in the design of follow-up experiments. Although multiple methods have been established that are based on stable-isotope labeling and label-free approaches, one of the remaining bottlenecks is the analysis and quantification of proteins in large datasets. MSQuant is a platform for protein quantification, capable of handling multiple labeling strategies and supporting several vendor data formats. Here, we report on the use and versatility of MSQuant.

Key words

Protein quantification Stable isotope labeling Quantitative proteomics Automation