Protein Analysis service

The Protein Analysis laboratory provides a protein identification and characterisation service for the London Research Institute. The techniques currently available are:

• Peptide Mass Fingerprinting (PMF)/High Energy CID:

  Routine protein identifications can be performed by obtaining a peptide mass fingerprint following in-gel digestion of bands or spots of interest with proteases such as Trypsin or Asp N.
  
  Using the ABI 4700 TOF-TOF instrument, peptide masses can be measured with an accuracy of < 10ppm. These are then searched against an in silico digest of the latest databases. Typically 60-70% of proteins can be identified by this method. Selected peptide ions from this first analysis can then be subjected to high-energy collision to obtain fragment ions. These MS/MS spectra can be used to identify the protein or proteins present in the sample.
  
  

• Peptide Sequencing by Ion-trap Mass Spectrometry:

  For more complex samples that need further studies, the peptides are subjected to analysis by nano-lc MS/MS.
  
  Peptides separated by reverse phase l.c. are sequenced by low energy collision induced fragmentation (CID) using a linear quadropole ion trap (Q-Trap 4000) using a nanoflow interface. MS/MS data is automatically searched against updated databases.
  
  

• Post Translational Modification (PTM) Projects:

  The service's ABI 4000 Q-Trap linear ion trap mass spectrometer and 4700 Maldi TOF-TOF are used to determine sites of modification such as phosphorylation.
  
  

• 2-D Gel Electrophoresis:

  Advice, equipment, reagents, and expertise for researchers to generate quality 2-D gel data on specialist equipment, allowing the reproducible running of 2-D gels. Scanning and software packages to enable analysis of 2-D gels are also available.

Head of the Protein Analysis laboratory is Nick Totty.