In this dissertation, we combine microfluidics and surface-enhanced Raman spectroscopy (SERS) in order to create a platform for identification of cells labeled with SERS biotags (SBTs) based their multiple surface biomarkers. Microfluidic systems allow us to transport cells to the detection region and control their advection with unprecedented control and precision. It also help us with faster processes using smaller sample quantities. In combination with a powerful chemical detection method such as SERS, a platform capable of multiplexed identification of cells can be developed.

SERS is a molecular identification method based on enhancement of molecules' vibrational spectra due to plasmonic resonances. Metallic nanostructures are needed to achieve unparalleled enhancements that render SERS capable of detection single molecules.

Here, we use a flow-focusing microfluidic device to transport cells and micron-sized particle to a SERS interrogation region and collect their signature in a cytometry fashion. Three labeling and data analysis schemes were developed:

• In the first platform, the concept of identification of SERS-labeled particles in a microfluidic channel was put to test. As a proof-of-concept, micron-sized beads labeled with different combinations of two tags was used and successfully identified by means of ratiometric analysis of SERS signals.

• In In the second system the two-tag platform was used in order to identify circulating prostate cancer cells in a background of normal prostate cells. In this system, one SBT was used as a universal tag and the second SBT was targeting a specific biomarker that is overexpressed in cancer cells. We managed to detect a population of 1% cancer cells in a mixture of cancer and normal cells.

Finally, a multiplexed SERS identification system was developed which enabled us to discriminate between four populations of microbeads that were labeled with multiple cocktails of four SBTs. This platforms can be used for various immunophenotyping application where cells with multiple surface biomarkers are targeted.