Exclude Custom Category from Custom Post Type Loop

Hello,

I have setup a custom post type that has multiple categories. However, I would like to setup the archive-custom.php file to hide a specific category.

I was sucessfully able to use the following code on the index.php page for the regular WordPress post type to exclude a category, but it does not seem to work for the custom post type/category.

<?php query_posts('cat=-4'); ?>
<?php if (have_posts()) : while (have_posts()) : the_post(); ?>

...Rest of Loop...

<?php endwhile; ?>

Is something different needed when using a custom post type/category?