$a = 'PF01389   6   218 1   255 430.09';
$b = 'PF00691   PF01389';

my %in_a    = map  { $_ => 1          } split /\s+/, $a;
my @in_both = grep { exists $in_a{$_} } split /\s+/, $b;

if ( @in_both ) {
    print "correct\n";
}