#!C:/Perl/bin/perl.exe -w 
 
open (Peptide1, "data.txt")|| die ("cannot open file"); 
@data = <Peptide1>; 
$i=0;$j=0; 
 
        foreach $dat(@data) 
        { 
                   while ($dat =~m/END IONS/) 
                { 
                 $daten[$j][$i]=$dat; 
                        $i++; 
 
                } 
                $j++; 
} 
 
close (Peptide1);

#!C:/Perl/bin/perl.exe 
use strict; 
use warnings; 
use Data::Dumper; 
*Peptide1 = *DATA; 
#open( Peptide1, '<', "data.txt" ) || die("cannot open file"); 
my @data = <Peptide1>; 
chomp @data; 
my @daten; 
close(Peptide1);  
 
my $i    = 0; 
my $j    = 0; 
foreach my $dat (@data) { 
    $daten[$i][$j] = $dat; 
    if ( $dat =~ m/END IONS/ ) { 
        $i++; 
        $j = -1; 
    } 
    $j++; 
} 
print Dumper @daten 
__END__ 
00 
01 
02 
03 
END IONS 
10 
11 
12 
13 
END IONS 
20 
21 
23 
END IONS