Missing an expected period is the first serious sign of pregnancy but it doesn't always mean that you are pregnant; a missed period could indicate another medical issue. Lack of menstruation (amenorrhea) can be doe to many other reasons beside pregnancy: functional ovarian cyst, hypogonadism, menopause etc. At your age (late 20's) a functional ovarian cyst is the most plausible reason for amenorrhea besides pregnancy. Nonetheless, that’s why a pregnancy test is always necessary to confirm or exclude pregnancy. In your case, it seems that a pregnancy is excluded because pregnancy test was negative. You can still do another pregnancy test. In fact, a blood based pregnancy test would be more accurate. And you can follow up with a gynecologist who can help you diagnose a functional ovarian cyst, if indeed, you are experiencing this.

P.S. The IUD is one of the most efficient contraceptive methods with an efficiency rate of over 98%.