This article is from the Astronomy FAQ, by Joseph Lazio (jlazio@patriot.net) with numerous contributions by others.
By Ron Baalke <baalke@kelvin.jpl.nasa.gov>,
contributions by Bill Owen <wmo@wansor.jpl.nasa.gov>,
edited by Steve Willner <swillner@cfa.harvard.edu>
Pluto was discovered from discrepancies in the orbits of Uranus and
Neptune. The search was for a large body to explain the
discrepancies, but Pluto was discovered instead (by accident, if you
will, though Clyde Tombaugh's search was systematic and thorough).
Pluto's mass is too small to cause the apparent discrepancies, so the
obvious hypothesis was that there is another planet waiting to be
discovered.
The orbit discrepancies go away when you use the extremely accurate
measurements of the masses of Uranus and Neptune made by Voyager 2
when it flew by those planets in 1986 and 1989. Uranus is now known
to be 0.15% less massive and Neptune 0.51% less massive, than was
previously believed.
[N.B. These numbers come from comparing the post-Voyager masses to those in
the 1976 IAU standard.]
When the new values for these masses is factored into the equations,
the outer planets are shown to be moving as expected, going all the
way back to the early 1800's.
The positional measurements do not bode too well for the existence of
Planet X. They do not entirely rule out the existence of a Planet X,
but they do indicate that it will not be a large body.
Reference:
Standish, E. M., Jr. 1993, "Planet X: No Dynamical Evidence in the
Optical Observations," Astronomical Journal, vol. 105, p. 2000--2006
 
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