while (<MS_file>){
	chomp;
	my ($to_be_peak, $intensity, $FWHM, $res) = split /\t/;
	if ($intensity >= $min){
		$_=$to_be_peak;
		s/(\d+)\.\d+/$1/; # removes the dps
		$peak=$_;
		#$peak = $to_be_peak;
		push(@peak_list, $peak);
	}
}
print MS_out "These results are from : $file\n";
print MS_out "These are the selected peaks\n@peak_list\n";

#---------------------------------------
#the value we want to start with - putting $peak_arrary into $val - and then printing it
for (my $d=0; $d<= @peak_list; $d++){
	$diff_peak[$d]=$peak_list[$d]-$peak_list[$d+1];
}
print "Diff_peak after @diff_peak\n";

for (my $j=0; $j<= @diff_peak;$j++){
	$val=$diff_peak[$j];
#	$val = 89; #test 
	print "This is val $val\n"; # test value
	&find_molecules($val, 0, \%a_result, $accuracy); # start function with new val
	#to print the results on your screen
	foreach my $rh_result(@list_of_results){
		foreach(keys %{$rh_result}){
			print MS_out ($_, "\t", $rh_result->{$_}, "\n");
		}
		print MS_out "*******************\n";
	}
	print MS_out "_________________End_of_Result_________________\n";
	foreach my $rh_result (@list_of_results){
		foreach (keys %{$rh_result}){
			$rh_result->{$_}=0;
		}
	}
}
print MS_out "/\/\/\ \n";
#--------------------------------------
#Now find the difference and find possiblitiess
sub find_molecules{
	my ($current_val, $current_index, $rh_result, $acc)= @_;
	#we go through all the element_masses, which weren't below equal or below zero before
	for(my $i=$current_index; $i<=$#element_masses; $i++){
		#if the current_val is equal the current element_mass
		if(!($current_val-$element_masses[$i])){
			#we add the result to the list_of_results
			my %a_result= %{$rh_result};
			$a_result{$element_masses[$i]}++;
			push @list_of_results, \%a_result;
			#if the difference is greater than zero, we keep on going
		}elsif($current_val-$element_masses[$i] >= $acc){
			my %a_result= %{$rh_result};
			#we add the current element_mass to the result hash
			$a_result{$element_masses[$i]}++;
			#and call ourselves with the new parameters..
			&find_molecules($current_val-$element_masses[$i], $i, \%a_result, $acc);
		}
	}
}

These results are from : Proline.txt
These are the selected peaks
117 116 71 70
1	1
16	0              # Normal!
12	0
14	0
*******************
_________________End_of_Result_________________
1	1
16	0              # Why does it do this?
12	0
14	0
*******************
1	1
16	2
12	1
14	0
*******************
1	13
16	2
12	0
14	0
*******************
1	1
16	1
12	0
14	2
*******************
A lot more file....
*******************
1	21
16	0
12	2
14	0
*******************
1	33
16	0
12	1
14	0
*******************
1	45
16	0
12	0
14	0
*******************
_________________End_of_Result_________________
1	1
16	0                   #Why does it do this?
12	0
14	0
*******************
1	1
16	2
12	1
14	0
*******************