The script below produces the same output as in your example output. Run it as follows (assuming the script is stored as z):

perl z tmp01 tmp02

It's formatted widespreadly for better readability.

#!/usr/bin/env perl

use strict;
use warnings;

my $seen;

while ( <> ) {
    next unless /^\d/;

    s/\s*$//;

    next unless m/        # [file1]    [file2]
        ^
        (\S+)        # PeptideID    PeptideID
        \s+
        (\S+)        # ProteinID    SpectrumID
        (?:
            \s+
            (\S+)    # -----        Sequence
        )?
        $
    /x;

    if ( $3 ) {
        $seen->{$1}->{SpectrumID} = $2;
        $seen->{$1}->{Sequence}  = $3;
    } else {
        push @{ $seen->{$1}->{ProteinID} }, $2;
    }
}

sub frmt {
    print join("\t", @_) . "\n";
}

frmt qw( PeptideID ProteinID SpectrumID Sequence );

foreach my $k ( sort { $a <=> $b } keys %{ $seen } ) {
    foreach my $p ( @{ $seen->{$k}->{ProteinID} } ) {
        frmt $k, $p, $seen->{$k}->{SpectrumID}, $seen->{$k}->{Sequence
+};
    } 
}
[download]