Optimization workflow for the processing of high quality glass-based microarrays: applications in DNA, peptide,...

As the performance of microarray experiments is directly dependent on the quality of the materials, the suitability of the protocols, and the accuracy of the work performed, optimization of existing microarray workflows is needed in almost every experiment to achieve higher quality and meaningfulness of the generated data. In the following, we describe a workflow for the optimization of microarray processing parameters, based on the previously selected surface structure. Four simple model experiments with dye-labeled compounds is used to determine crucial experimental parameters including spotting concentration, spotting solution, immobilization efficiency, and blocking conditions even in cases where recommendations from the slide manufacturer or from the literature are missing. In this article, processing parameters for DNA, peptide, antibody, and carbohydrate microarrays are outlined. The applicability of the model experiments is demonstrated and described in detail on the example of short oligonucleotides.