Databases comparing expressed sequence

The major advantage of the tandem mass spectrometry approach compared to MALDI peptide fingerprinting, is that the sequence information obtained from the peptides is more specific for the identification of a protein than simply determining the mass of the peptides. This permits a search of expressed sequence tag nucleotide databases to discover new human genes based upon identification of the protein. This is a useful approach because, by definition, the genes identified actually express a protein. 

Partial Hydrolysis and Sequence Comparison In some cases it is also possible to determine the sequence of an unknown polypeptide by sequencing just a few of its amino acids and comparing this partial sequence with the database of known sequences for complete polypeptides or proteins. This procedure works if the unknown peptide turns out to be one that has been studied previously. (Studies of the expression of known proteins is one dimension of the field of proteomics. Section 24.14.) Due to the many sequence permutations that are theoretically possible and the uniqueness of a given proteins structure, a sequence of just 10—25 peptide residues is usually sufficient to generate data that match only one or a small number of known polypeptides. The partial sequence can be determined by the Edman method or by mass spectrometry. For example, the enzyme lysozyme with 129 amino acid residues (see Section 24.10) can be identified based on the sequence of just its first 15 amino acid residues. Structure determination based on comparison of sequences with computerized databases is part of the burgeoning field of bioinformatics. 

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