One main application for protein and peptide microarrays is the identification of antibodies in patient serum. These may be disease-related antibodies, such as those of type IgG and IgM associated with cancerous diseases or rheumatism, or antibodies associated with allergies (type IgE), or those against bacterial or viral infections. Depending on the area of inquiry, proteins, parts of proteins as peptides or the entire (sub)proteome are immobilized on a microarray and incubated with serum. Detection is performed by using specific antibodies against the corresponding IgG family. When required, the serum can be purified and the slide can be incubated with the standardized concentration of IgGs. Along with a meticulous selection of potential antigens, the selection of the patient sera is a critical factor. Selection, in this context, means a potential stratification of patients into subfamilies, the selection of the corresponding control patient cohorts, the number of patients, the time at which the samples are collected, and the way sera are prepared and stored, starting with sample collection and through to transport and analysis. Using these factors as a basis, microarrays can be a highly informative instrument to identify and validate disease-related biomarkers.
In addition, microarrays like this can be used to determine serotypes, and when transplants are performed, the data can be used as a basis for predicting the compatibility or the risk of rejection of the transplant. To date, well over 1,000 different HLA genotypes have been described. Only around 100 genotypes are available as proteins for analysis. This limitation is due to the complicated expression and purification of proteins, for which the 3-dimensional conformation must be retained. In this case, protein microarrays or peptide microarrays with peptide cycling can be a valuable instrument to overcome these limitations.