Searching With Tandem Mass Spectrometric Data.
Database can also be examined for similarities with tandem mass spectrometric data obtained on peptides from the protein of interest. Because tandem mass spectra contain structural information related to the sequence of peptide, rather than only its mass, these searches are more reliable and specific. Several approaches exist, one of the most important approaches being the peptide sequence tag method. It makes use of the fact that nearly every tandem mass spectrum contains at least a short run of fragment ions that unambiguously specify a short amino acid sequence. Such a peptide sequence tag will then be used to retrieve the corresponding  sequence from the database. The procedure can be automated and is highly specific, especially when performed using instrument, such as quadrupole TOF.