Abstract: A microplate reader simultaneously obtains Raman measurements from samples contained in non-adjacent wells. At least two Raman probes are positioned perpendicularly above or below the microplate to simultaneously acquire Raman spectra data of the non-adjacent liquid samples. Each probe is coupled to a laser and a spectrometer and includes a lens focusing laser light within the sample and collecting light from the sample for the spectrometer. The spectrometer may include a 2D imaging sensor (sCMOS or CCD) to image light from multiple probes simultaneously, spaced from one another to reduce crosstalk. A positioner moves the microplate plate or probes to acquire data from a different subset of non-adjacent samples, and may also vary laser focus within wells during data acquisition. Multiple fluorescence probes may simultaneously acquire fluorescence data from the same samples, or non-adjacent samples. Probes may be fiber-coupled and positioned within a reaction chamber of a liquid handling system.