Protein Identification by MALDI-TOF Mass Spectrometry

  • Judith Webster
  • David OxleyEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 800)


MALDI-TOF mass spectrometers are now commonplace and their relative ease of use means that most non-specialist labs can readily access the technology for the rapid and sensitive analysis of biomolecules. One of the main uses of MALDI-TOF-MS is in the identification of proteins, by peptide mass fingerprinting (PMF). Here we describe a simple protocol that can be performed in a standard biochemistry laboratory, whereby proteins separated by 1D or 2D gel electrophoresis can be identified at femtomole levels. The procedure involves excision of the spot or band from the gel, washing and destaining, reduction and alkylation, in-gel trypsin digestion, MALDI-TOF-MS of the tryptic peptides and database searching of the PMF data. Up to 96 protein samples can easily be manually processed at one time by this method.

Key words

Proteomics MALDI-TOF Mass spectrometry SDS-PAGE 2D-gel In-gel digestion Peptide mass fingerprint Protein identification Database searching 



The authors acknowledge the support of the Biotechnology and Biological Sciences Research Council, UK.


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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Proteomics Research Group, Babraham InstituteBabrahamUK

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