1. A computer-implemented method of generating reference spectra, comprising: polishing a first substrate in a polishing apparatus having a rotatable platen; measuring a first sequence of spectra from the first substrate during polishing with a first in-situ monitoring system; associating each spectrum in the first sequence of spectra with an index value equal to a number of platen rotations at which the each spectrum was measured; storing the first sequence of spectra as reference spectra; receiving data from a second in-situ monitoring system that monitors the first substrate during polishing of the first substrate; detecting a polishing endpoint of the first substrate during polishing of the first substrate based on the data from the second in-situ monitoring system and without accessing data from the first in-situ monitoring system to detect the polishing endpoint; determining a target index value based on the number of platen rotations at the time the polishing endpoint is detected by the second in-situ monitoring system; polishing a second substrate in the polishing apparatus; measuring a second sequence of spectra from the second substrate during polishing with the first in-situ monitoring system and without the second in-situ monitoring system; and adjusting a polishing parameter for at least one zone on the second substrate to adjust a polishing rate of the at least one zone based on the reference spectra, the second sequence of spectra, and the target index value.