A major application of protein and peptide microarrays is the identification of antibodies in patient serum. This can be disease-associated antibodies, e.g. for cancer and rheumatism of the IgG and Ig M type, but also antibodies for allergies (type IgE) or against bacterial and viral infections. Depending on the problem, the proteins, parts of the proteins as peptides or the entire (sub-)proteome are immobilized on a microarray and incubated with serum. Detection is performed by means of specific antibodies against the corresponding IgG family. If necessary, the serum can be purified and the slide incubated with the concentration normalized IgGs. Besides a careful selection of potential antigens, the selection of patient sera is a critical factor. Selection here means a possible stratification of patients into subfamilies, the selection of the appropriate control patient cohort, the number of patients, the time of sampling(s) and the preparation and storage of the sera from sampling to transport and analysis. Based on these factors, microarrays can be a very powerful tool to identify and validate disease-associated biomarkers.
In addition, such microarrays can be used to determine serotypes and, based on the data obtained during transplantation, to make a prediction of the tolerance or risk of graft rejection. To date, well over 1,000 different HLA genotypes have been described. Only about 100 genotypes are available as proteins for analysis. The limitation here is the complex expression and purification of the HLA proteins, where the 3-dimensional conformation must be preserved. Protein microarrays or peptide microarrays with cyclized peptides can be a valuable tool to overcome these limitations.