Protein Identification by MALDI

Protein Identification by MALDI

Protein Identification by MALDI-TOF/TOF (PMF + MS/MS)

Proteins are digested with trypsin (cleaves at R-X and K-X except when X is Pro) and the sample is then analysed by MALDI-TOF, generating a peptide mass fingerprint for the protein. The most abundant peptide ions are then subjected to MALDI-TOF/TOF analysis, providing information that can be used to determine the sequence. The results from both types of analysis are combined and searched using software (e.g. Mascot) against protein, DNA or EST databases, to identify the protein.

Recommended for:

The identification of known purified proteins. i.e. simple gel bands.


  • Rapid analysis and turn around time (similar to MALDI-TOF)
  • High sensitivity
  • Relatively inexpensive
  • Suitable for large numbers of samples
  • Able to identify 2-3 proteins in the same spot
  • Sequence information provides confirmation of peptide mass fingerprint identification
  • Sequence information allows identification of small proteins (<15kDa)


  • Sequence information generally not as complete as that provided by LC/MS/MS
  • Limited success in identification of proteins that are not in the database

For further details or advice on this APAF service please contact us at

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