Peptide Sequence Tags (PSTs) (Mann94) can be easily generated from MS/MS spectra analysis. A PST is defined as a short peptide sequence (3 to 5 amino acids) flanked by two masses corresponding to the two adjacent polypeptides.

Peptide Sequence Tag

These two masses give information on the two unknown sub-sequences corresponding to the spectrum areas that are not easily interpretable. Using PSTs as results of mass spectrometry analysis offers several advantages:

 Only few peaks (n+1 where n is the size of the PST sequence) are needed for the PST determination that is therefore more easy to obtain than the complete peptide sequence (especially when the spectrum is noisy).

 Generating several overlapping PSTs from one spectrum may contribute to produce de-novo-sequencing-like results while avoiding the frequent misinterpretations due to de-novo algorithms.

 From the algorithmic point of view, rapid pattern-matching of short PST sequences can be achieved very efficiently since the small size of PST sequences allow to use hash-coding techniques.