You can't apply JS only to one browser using Drupal functions. What you can do is:
CSS workaround:
- apply CSS only to IE
- assign some style that will not be visible, but also will not be present in non-IE, like white 1px border on white background
- use
css()
jQuery method to test if element has property you expect it to have in IE, and if true, execute your code.
JavaScript way: Use jQuery Browser Plugin or similar solution to identify browser inside your js file. Execute your code if it's the browser you need it executed in.