We have developed an ISA (individual-specific autoantibody) identification method to identify biological samples based on an individual's unique class of autoantibodies. This method involved the presentation of human proteins derived from crude lysates after SDS/PAGE separation and transferance to a solid support. In the present study, ISA strips are produced and developed on a new protein microarray. In making the ISA strips, it was found that variation in protein migration during electrophoresis and strip-manufacturing quality control limit the reliability of the assay. Therefore it was decided to semi-purify and separate proteins by column chromatography in large batches and to develop an ISA-specific protein microarray. It was found that this ISA protein microarray approximates a similar serum titre as the ISA strip and is predicted to circumvent the batch-to-batch production issues related to SDS/PAGE.