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J Biomol Tech. 2010 September; 21(3 Suppl): S10.
PMCID: PMC2918161

Proteomics I: MS-Based Workflows and Sample Preparation

D. Fenyö1 and R.S. Annan2
1Rockefeller University, New York, NY, United States;
2GlaxoSmithKline, King of Prussia, PA, United States;
3New York University School of Medicine, New York, NY, United States



Proteomics experiments are designed to provide useful information about the biological system under study. As mass spectrometry technology and methodology have improved, many or most of these studies now focus on relative or absolute quantitation of proteins and their posttranslational modifications under more than one experimental condition in order to do this. The goal of this workshop is to provide an overview of possible proteomic strategies for relative or absolute quantitation of proteins that are suitable for a given purpose. We also hope to provide practical advice for experimental design and sample preparation for quantitative studies and characterization of posttranslational modifications. Issues to be covered include requirements for protein sequence coverage, discovery vs. directed (verification) approaches, strategies for chemical and metabolic labeling as well as label free methods, introduction to relevant informatics approaches for quantitation studies, and sample preparation and enrichment for posttranslational modification studies.

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