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Mass Spectrometry for Peptide and Protein Analysis

Peptides and Proteins

  1. Mark W. Duncan1,
  2. David S. Gibson2

Published Online: 17 DEC 2012

DOI: 10.1002/9780470027318.a9199

Encyclopedia of Analytical Chemistry

Encyclopedia of Analytical Chemistry

How to Cite

Duncan, M. W. and Gibson, D. S. 2012. Mass Spectrometry for Peptide and Protein Analysis. Encyclopedia of Analytical Chemistry. .

Author Information

  1. 1

    University of Colorado Denver, Aurora, CO, USA

  2. 2

    Queen's University of Belfast, Belfast, UK

Publication History

  1. Published Online: 17 DEC 2012


Mass spectrometry is playing an increasingly important role in the characterization and quantification of peptides and proteins. In fact, more conventional approaches to characterization, including techniques such as Edman sequencing and amino acid (AA) analysis, have been largely displaced. Mass analysis — following either matrix-assisted laser desorption ionization (MALDI) or electrospray ionization (ESI) — offers rapid molecular mass determinations with high mass accuracy on subpicomole amounts of material and information can be obtained on the constituents of complex mixtures.

The application of tandem mass spectrometry (MS/MS) allows fragmentation of peptide ions, and of proteins with some enhancements too. The MS/MS spectra of peptides and proteins can interpreted de novo or matched against database entries to provide partial amino acid sequence information and peptide/protein identification. Both peptide-centric (bottom-up) and protein-centric (top-down) approaches to protein characterization have been adopted and are now routinely applied.

Mass spectrometry has also been pivotal to the development and wide application of proteomics: i.e. the large-scale identification of the proteins present in a complex biological sample. Proteomics is now routinely applied to characterize and quantify the constituents of complex biological tissues and fluids.

This entry describes the available approaches to peptide and protein characterization based on mass spectrometry, the constantly evolving analytical methods for proteomics, and available strategies for protein quantification.