The general problem here is that modifier keys like <CTRL> and <ALT> are being interpreted by the tty itself.  You could try something like this, however:

#!/usr/bin/perl

use Term::ReadKey;

my $my_sequence = qr/\x1b\x02\z/;  # <CTRL>+<ALT>+B
my $key;
my $key_buf;

ReadMode 4;
while ($key ne 'q') {
    $key = ReadKey();
    printf "key=\\x%02x\n", ord($key);  # debug
    $key_buf .= $key;
    if ($key_buf =~ $my_sequence) {
        system "xmessage 'OH YA!'";
        last;
    }
};
ReadMode 0;
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This has its limits, too (for example I wouldn't know how to tell apart <CTRL>+<ALT>+B from <CTRL>+<ALT>+<SHIFT>+B), but maybe it's sufficient for your purpose.

<CTRL>+A .. <CTRL>+Z typically maps to 1..26 (ord($key), that is); and <ALT>+... typically generates a two-byte sequence with a leading ESC (27 or \x1b). Other keys (cursor keys, etc.) generate three-byte sequences...

Printing out the sequence you get when you hit a certain key/modifier combination will tell you which substring to match (you don't necessarily need a regex for this, btw; index() would do).  But in case portability is an issue, be aware that terminals sometimes differ with respect to the sequences they generate — in particular the multi-byte ones...

Update: the loop exit condition ($key eq 'q') is probably too simple for production use (it would also exit on hitting <ALT>+q, for example, due to the second byte of the escape sequence being 'q')...  Fixing this is left as an exercise for the reader :)