c:\@Work\Perl\monks>perl -wMstrict -MData::Dump -le
"my @proteins = qw(AAAAKAAAA AAAAKAAAA AAAAAA);
 ;;
 my %seen = map {$_ => 1} @proteins;
 ;;
 print qq{Peptide '$_'}
   for grep !$seen{$_}++, map {split /[KR]\K(?!P)/} @proteins;
 ;;
 dd \%seen;
"
Peptide 'AAAAK'
Peptide 'AAAA'
{ AAAA => 2, AAAAAA => 2, AAAAK => 2, AAAAKAAAA => 1 }