Does the annual limit apply to me if I hold a Master's degree?

Yes, the numerical cap on H-1Bs applies to master's degree holders except that those who obtained their master's degree in the United States are allotted an additional 20,000 H-1B visas annually.  As such U.S. Master's degree holders may continue applying for H-1B visas after the expiration of H-1B visas for others.