yes, you can use your different advanced degree.

You are eligible to 20000 cap using your advanced degree issued by a accredited US institution.

But you need a BS that is related to your field of employment in order to be qualified for H1b application.


http://www.ofwguide.com/article_item.php?articleid=289

Q: I have a master’s degree earned in the U.S. in a different field than my H-1B position. For example, I have a master’s degree from UCLA in history and a B.S. in Computer Engineering from the Philippines, and I will be working as a software engineer. Can I get the advanced degree H-1B?

Yes. The USCIS has stated that the advanced degree to qualify for the separate 20,000 H-1B visa category does not need to be in offered field of employment.