A method of Raman detection for a portable, integrated spectrometer instrument includes directing Raman scattered photons by a sample to an avalanche photodiode (APD), the APD configured to generate an output signal responsive to the intensity of the Raman scattered photons incident thereon. The output signal of the APD is amplified and passed through a discriminator so as to reject at least one or more of amplifier noise and dark noise. A number of discrete output pulses within a set operational range of the discriminator is counted so as to determine a number of photons detected by the APD.