ABSTRACT
Several different strategies are applicable in the computer-based searching of sequence databases for the identification of unknown proteins. The choice of strategy employed is often dictated by the format of the data available. However, one must always use caution and examine the results with a critical eye. It is the responsibility of the investigator to examine the list of resultant matches with respect to quality of fit. Often this is aided by examining the individual MS/MS spectra and ensuring that most of the abundant ions are being used for identification, not simply those that are in the “grass.”
