The PCL has a ThermoFinnegan DecaXP ion trap mass spectrometer that is used solely for peptide analysis, protein ID and de novo protein sequencing for protein identification using nano-spray LC/MS/MS. Typically, protein digests are separated by capillary rp-HPLC prior to in-line analysis of their masses and fragmentation patterns.
The masses of the parent ions and their fragments are used to search databases of known proein sequences to match to in silico digestion patterns of the proteins. Matches are made using search algorithms for goodness of fit and scored. The PCL uses in-house TurboSequest and MASCOT search engines and databases for protein identifications.
Please contact the PCL prior to submitting samples for this analysis. Sample preparation is critical to the success of this technique as is the availability of a sequenced genome of the experimental organism.