c:\@Work\Perl\monks>perl -wMstrict -le
"my @proteins = qw(
   DAAAAATTLTTTAMTTTTTTCKMMFRPPPPPGGGGGGGGGGGG
   ALTAMCMNVWEITYHKGSDVNRRASFAQPPPQPPPPLLAIKPASDASD
   AAAKAAA  AAAKAAA  XXXXXX
   );
 ;;
 my @new_peptides;
 for my $protein (@proteins) {
   if ($protein =~ s{ (?<= [KR]) (?! P) }{=}xmsg) {
     push @new_peptides, split ('=', $protein);
     }
   }
 ;;
 for my $peptide (@new_peptides) {
   print qq{Peptide is '$peptide'};
   }
"
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'