Methods for evaluating probe arrays

A method of evaluating an amount of a target substance comprising the steps of:

• reacting a probe away and the target substance which is previously labeled, wherein the probe array comprises a plurality of probes immobilized at a plurality of matrix sites on a substrate for capturing the target substance, the plurality of probes is sequentially synthesized at the plurality of matrix sites on the substrate to a desired length, each of the plurality of probes is different from each other, and a labeling compound is coupled to each terminus of the plurality of probes in a final step of the sequential synthesis;
• measuring an amount of the labeling compound at each of the plurality of matrix sites to determine an amount of the probe at each of the plurality of matrix sites;
• measuring an amount of the labeled target substance captured by the probe at each of the plurality of matrix sites;
• measuring an amount of the labeling compound directly bonded to the substrate at a predetermined matrix site on the surface of the substrate, wherein no probes are immobilized at the predetermined matrix site, and wherein the labeling compound is directly bonded to the substrate during a first step of the sequential synthesis without an elongation reaction;
• comparing the amount of the probe, the amount of the labeled target substance, and the amount of the directly bonded labeling compound,
• wherein all probes forming the probe array have the labeling compound coupled to their termini.