A system for laser scanning provides spectral flexibility needed for the spectroscopic monitoring of highly multiplexed samples, such as cellular and particle assays in whole blood or other suspensions. In accordance with embodiments of the present invention, the system comprises a scanner to direct an excitation laser through a sample, an objective to collect light emitted by the sample in response to the excitation laser, a spectrograph to disperse the emitted light over a plurality of wavelengths as a spectrum, and a charge coupled device for detecting the spectrum. The system can be used with samples having a variety of reporter tags, including one or more SERS tags, fluorescent organic and protein tags, and quantum dot tags. A laser scanning apparatus and method of using the same is also provided.