...
while (<DATA>)
...

__DATA__
>some:header|text|foo:bar|blah
WHATEVER:DATA|WOULD:DEMONSTRATE|THE:PROBLEM
...

##</code><code>##

    foreach $value (@e) {
        my @elements= split(/\|/, $value);
        ...  
#  next 2 lines assume that $value had at least 6 strings
#  separated by "|" (but maybe it only had 2):
        my @missedc = split (/:/, $elements[2]);#60
        ...
        my @s = split(/:/, $elements[5]);#62
        my $sequence = $s[1];
# when the assignment to @s warns and fails (because 
# @elements < 6) the next line will also warn and fail:
        my @peptides = split (/ /, $sequence);#65
        ...
# and so will this line:
        my $output = "$headers[1]\t\t$peptide\t\t$total \t\t 1 \t\t$missed\t$sequence\n";#72
        ...
    }