c:\@Work\Perl\monks>perl -wMstrict -le
"my @proteins = qw(
   DAAAAATTLTTTAMTTTTTTCKMMFRPPPPPGGGGGGGGGGGG
   ALTAMCMNVWEITYHKGSDVNRRASFAQPPPQPPPPLLAIKPASDASD
   AAAKAAA  AAAKAAA  XXXXXX
   );
 ;;
 my $cleave = qr{ (?<= [KR]) (?! P) }xms;
 ;;
 my @peptides =
   map  split($cleave),
   grep m{ $cleave }xms,
   @proteins
   ;
 ;;
 print qq{Peptide is '$_'} for @peptides;
"
Peptide is 'DAAAAATTLTTTAMTTTTTTCK'
Peptide is 'MMFRPPPPPGGGGGGGGGGGG'
Peptide is 'ALTAMCMNVWEITYHK'
Peptide is 'GSDVNR'
Peptide is 'R'
Peptide is 'ASFAQPPPQPPPPLLAIKPASDASD'
Peptide is 'AAAK'
Peptide is 'AAA'
Peptide is 'AAAK'
Peptide is 'AAA'