Chemical Genomics

Volume 310 of the series Methods in Molecular Biology™ pp 227-240

Peptide Mass Fingerprinting

Protein Identification Using MALDI-TOF Mass Spectrometry
  • Judith WebsterAffiliated withProteomics Research Group, Babraham Institute
  • , David OxleyAffiliated withProteomics Research Group, Babraham Institute

* Final gross prices may vary according to local VAT.

Get Access


Matrix-assisted laser desorption/ionization (MALDI)-time-of-flight (TOF)-mass spectrometry (MS) is now routinely used in many laboratories for the rapid and sensitive identification of proteins by peptide mass fingerprinting (PMF). We describe a simple protocol that can be performed in a standard biochemistry laboratory, whereby proteins separated by one- or two-dimensional gel electrophoresis can be identified at femtomole levels. The procedure involves excision of the spot or band from the gel, washing and de-staining, 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