The following article contains a link to the homepage for the X! Tandem search engine. X! Tandem can be run inside Scaffold 5/Q+S to increase confidence in peptide identifications: X! Tandem.
Please note the following:
When a peptide starts with E or Q, TANDEM automatically checks for the formation of pyroglutamic acid, i.e., the loss of water or ammonia, respectively. This modification happens spontaneously in solution and failure to test for it can result in missing significant peptide hits. The analogous reaction for iodoacetimide blocked cysteine (loss of ammonia) is also considered. This modification is considered to be an N-terminal modification only, so it does not affect any potential modifications specified for Q, E or C.