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Microfluidic chip-based liquid-chromatography coupled to mass spectrometry (LC-MS) has played an important role in proteomic research for high throughput analysis.Up to date, the use of chip-based LC-MS for quantitative determination of small molecules, such as active pharmaceutical ingredients (APIs) and abused drugs/drug metabolites, in pharmaceutical and clinical applications has not been thoroughly investigated.This paper will discuss the utilization of chip-based LC-MS systems for quantitative determination of small molecules (including abused drugs/drug metabolites and disease/tumor-associated biomarkers) for bioanalytical application.A integrated chip-nanoLC device integrates a microfluidic switch, a chip column design having a pre-column (enrichment column) for sample enrichment prior to an analytical column for separation, as well as a nanospray emitter on a single polyimide chip was utilized in this study.The approach to minimize ion suppression of urine sample will be presented; furthermore, the stability and lifetime of chip will be evaluated.In addition, the applicability of microfluidic chip-based LC-MS for the analysis of aflatoxins in food matrix will also be demonstrated.