Denovo Peptide Sequencing:
Even though a number of model organism genomes have been determined there still exists unknown genomes. In the case of organisms which have an uncharacterized genome traditional database correlational MS and MS/MS analysis does not work. In these cases peptides need to have their actual sequence determined via de novo MS/MS analysis. This is typically difficult to do because of the varied types of fragments that one gets in a typical MS/MS spectra. One way to circumvent this problem is to derivitize peptides with a chemical reagent such as 4-sulfophenyl isothiocyanate (SPITC). The derivitized peptides are analyzed via MALDI TOF TOF PSD (Post-Source-Decay) which produces MS/MS spectra with simplified fragmentation patterns (y type ion series) that can be easily interpreted. Once de novo sequences are determined they can be compared to the databases with homology based programs such as BLAST.
Wang, D., Kalb, S.R., Cotter, R.J. (2004) Rapid Commun. Mass Spectrom . 18: 96-102.
SPITC derivitized top panel and un-derivitized bottom panel MS/MS spectra of a tryptic peptide (1868 Da) from unknown Porcine sperm protein on Axima TOF2. Note the enhanced y ion series after derivitization which facilitates de novo sequence interpretation.