Overview of Peptide and Protein Analysis by Mass Spectrometry

Guoan Zhang1, Roland S. Annan2, Steven A. Carr3, Thomas A. Neubert1

1 Kimmel Center for Biology and Medicine, Skirball Institute and Department of Pharmacology, New York University School of Medicine, New York, New York, 2 Proteomics and Biological Mass Spectrometry Laboratory, GlaxoSmithKline, King of Prussia, Pennsylvania, 3 Broad Institute of MIT and Harvard, Cambridge, Massachusetts
Publication Name:  Current Protocols in Protein Science
Unit Number:  Unit 16.1
DOI:  10.1002/0471140864.ps1601s62
Online Posting Date:  November, 2010
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Mass spectrometry is an indispensable tool for peptide and protein analysis owing to its speed, sensitivity, and versatility. It can be used to determine amino acid sequences of peptides, and to characterize a wide variety of post‐translational modifications such as phosphorylation and glycosylation. Mass spectrometry can also be used to determine absolute and relative protein quantities, and can identify and quantify thousands of proteins from complex samples, which makes it an extremely powerful tool for systems biology studies. The main goals of this unit are to familiarize peptide and protein chemists and biologists with the types of mass spectrometers that are appropriate for the majority of their analytical needs, to describe the kinds of experiments that can be performed with these instruments on a routine basis, and to discuss the kinds of information that these experiments provide. Curr. Protoc. Protein Sci. 62:16.1.1‐16.1.30. © 2010 by John Wiley & Sons, Inc.

Keywords: proteomics; mass spectrometry; review

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Table of Contents

  • Why is Mass Spectrometry an Essential Tool in Peptide and Protein Analysis?
  • What is Mass Spectrometry?
  • What is Tandem Mass Spectrometry?
  • The Key Ionization Methods and Related Ancillary Techniques for Biomolecule Analysis
  • Mass Analyzers
  • Sample Preparation Prior to Ms
  • Bottom‐Up and Top‐Down Approaches
  • Protein Identification
  • Post‐Translational Modifications
  • Protein Quantitation
  • Fundamentals of Mass Measurement Accuracy and Mass Resolution Relevant to Biomolecule Analysis
  • Outlook
  • Acknowledgement
  • Literature Cited
  • Figures
  • Tables
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