Mass spectrometry (MS) provides quantified information to identify unknown atom and molecules which has become a widely used analytical technique in bioanalysis field. Polymer-based microfluidics device provides benefits of low fabrication cost, fast analysis time and less sample consumption for biological sample process and separation prior to MS analysis. In this dissertation, a table-size, computer-controlled robotic spotting system was developed to couple polymer microfluidics with mass spectrometry as an automatic and high throughput interfacing method. To accomplish this goal, three major subjects, polymer microfabrication, high sensitivity MS target substrate and polymer microfluidics / mass spectrometry interfacing were further evaluated and developed. First, polymer microfabrication techniques such as hot embossing and polymer bonding were discussed. Among those, a novel bonding technique of using UV/Ozone surface treatments for achieving low temperature bonds between poly(methyl methacrylte) (PMMA) and cyclic olefin copolymer (COC) microfluidic substrates is demonstrated. Second, a novel high sensitivity silicon-based matrix-free LDI-MS target substrate, nanofilament silicon (nSi) surfaces, was demonstrated in this dissertation. With electrowetting on nSi surfaces, it is demonstrated as a novel approach for preparing nSi based LDI-MS targets for the analysis of complex peptide samples. Finally, off-line integration of multiplexed polymer microfluidic interfacing with mass spectrometry by direct and automated spotting of peptide sample from multiplexed polymer microfluidic chip is demonstrated as a simple and robust method with uniform spotting volume and MS signal. This automatic contact spotting system is further demonstrated coupling with on-chip peptide reverse phase liquid chromatography (RPLC) separation with nSi surface as a novel microfluidics/ off-line mass spectrometry analysis.