c:\@Work\Perl\monks>perl -wMstrict -le
"use Data::Dump qw(dd);
 ;;
 my @proteins = qw(
   DAAAAATTLTTTAMTTTTTTCKMMFRPPPPPGGGGGGGGGGGG
   ALTAMCMNVWEITYHKGSDVNRRASFAQPPPQPPPPLLAIKPASDASD
   DAAAAATTLTTTAMTTTTTTCK
   XXXXXXX
   );
 ;;
 my %protein_peptides;
 ;;
 for my $protein (@proteins) {
   my @peptides = split /(?<=[KR])(?!P)/, $protein;
   ;;
   next if @peptides < 2;
   ;;
   push @{ $protein_peptides{$protein} }, \@peptides
   }
 ;;
 dd \%protein_peptides;
"
{
  ALTAMCMNVWEITYHKGSDVNRRASFAQPPPQPPPPLLAIKPASDASD => [
    ["ALTAMCMNVWEITYHK", "GSDVNR", "R", "ASFAQPPPQPPPPLLAIKPASDASD"],
    ],
  DAAAAATTLTTTAMTTTTTTCKMMFRPPPPPGGGGGGGGGGGG      => [
    ["DAAAAATTLTTTAMTTTTTTCK", "MMFRPPPPPGGGGGGGGGGGG"]
    ],
}