Overview
Searches are not constrained for only tryptic peptides, and indexed databases (databases only containing tryptic peptides) are not used. In cases where there are very complex mixtures, such as cell lysates, nonspecific cleavages can occur. Therefore, nontryptic peptides would be missed in the database search.
David M. Schieltz, Michael P. Washburn, and Lara G. Hays
Details
Details of this protocol, The Use Of Mass Spectrometry In Proteomics: Database Searching (Subscription Required), are located on a web site other than Biocompare Protocols.