New strategies for the high-throughput determination of protease substrate specificity using a dual colour microarray based format with a small library of FRET-based peptides were developed. Integral to this process was the development of an in-house hydrophobic microarray platform and the application of microarrays of microwells. Overall this allowed the rapid and quantitative analysis of a range of peptides with three proteases, subtilisin, chymopapain and thermolysin. An immobilised tetrafluoroarylsulfonyl chloride linker was developed to be used as a traceless linker for microwave-assisted palladium chemistry, namely transfer hydrogenation and deuteration, and Heck, Stille, Suzuki-Miyaura and Buchwald-Hartwig cross-coupling reactions. Palladium-mediated protocols under microwave irradiation were performed, allowing transfer hydrogenation and deuteration, and Suzuki-Miyaura and Heck cross-couplings.