A microfluidic approach is developed to automate and simplify multiplexed metabolite assays. Solid matrix assisted laser desorption ionization mass spectrometry (SMALDI-MS) on nanoporous thin films is suitable for analyzing small molecules, particularly metabolites, with a simple spot test. We present a system for blood sample preparation for metabolite analysis using centrifugal fluidics, coupled with derivatization and SMALDI-MS. This centrifugal microfluidic device enables semi-automated on-chip cleanup of blood samples, delivering a clean matrix for MS detection. A derivatization reagent is applied in our work to label the target molecules with fluorous affinity tags, so that higher S/N is observed by SMALDI-MS.