UNIT 16.1 Overview of Peptide and Protein Analysis by Mass Spectrometry

  1. Steven A. Carr,
  2. Ronald S. Annan

Published Online: 1 MAY 2001

DOI: 10.1002/0471140864.ps1601s04

Current Protocols in Protein Science

Current Protocols in Protein Science

How to Cite

Carr, S. A. and Annan, R. S. 2001. Overview of Peptide and Protein Analysis by Mass Spectrometry. Current Protocols in Protein Science. 4:16.1:16.1.1–16.1.27.

Author Information

  1. SmithKline Beecham Pharmaceuticals, King of Prussia, Pennsylvania

Publication History

  1. Published Online: 1 MAY 2001
  2. Published Print: JUN 1996

This is not the most recent version of the article. View current version (1 NOV 2010)


One goal of this introductory overview is to try and dispel the still widely held, but now mistaken, belief that mass spectrometry is beyond the technical resources of the typical laboratory or facility engaged in the structural characterization or synthesis of peptides and proteins. Over the last five years, mass spectrometers and associated data systems have become available that can be operated by anyone capable of running a modern amino acid analyzer or Edman sequencer, yet are powerful enough to handle the most demanding analyses that the peptide or protein investigator might require. The remaining goals of this article are to familiarize peptide and protein chemists 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. The emphasis here is on established tools and techniques that can realistically be used for problem solving. As a result, many useful instruments and techniques employed by the trained mass spectroscopist are not discussed here, because they do not satisfy these criteria or are not yet widely available; however, a few of these are briefly mentioned at the end of the unit. The overview concludes with a tutorial discussion on the meaning and practical importance of a number of fundamental experimental and performance-related issues that have important implications for interpretation and use of mass spectral data, such as mass accuracy and resolution.