We have developed microfluidic devices for high-throughput quantitative studies of protein interactions. In order to enable the measurement of transient molecular interactions we invented a novel detection mechanism based on mechanically induced trapping of molecular interactions (MITOMI) which we applied to measure the binding energy landscape of transcription factors. More recently we applied MITOMI to molecular diagnostics enabling the multiplexed analysis of protein biomarkers in a variety of sample matrices. Our most recent platform integrates digital MITOMI for single molecule detection with our standard MITOMI detection mechanism leading to high-sensitivity and dynamic range. The platform can measure up to 16 biomarkers in parallel from a small (5uL) whole blood sample obtainable via a simple pin-prick. In order to deploy the assay in point-of-care or resource limited environments we also engineered a low-cost instrument controlling the device and explored the use of cheap USB fluorescent microscopes for device readout. We applied this platform to the detection of Ebola specific IgG molecules in human serum sample and show that our platform can also distinguish different Ebola strain.