Proteomics and the analysis of protein sequences
One of the most widely used strategies in proteomics is correlative database searching. As discussed in Chapter 3, this involves searching the sequence databases for proteins containing peptides that match experimental data obtained by mass spectrometry, and when successful it results in deﬁnitive protein identiﬁcation. However, sequence analysis can provide a great deal more information than simple identiﬁcation. By comparing the sequence of a protein to all the other sequences that are stored in the databases, a researcher can ﬁnd information about protein structure, interactions, biochemical activity and evolution, and even a potential role in disease. Indeed, in the current post-genomics era, database searching based on protein sequence similarity often provides the ﬁrst leads in the elucidation of protein function.