Protein biomarkers are critical for drug target identification, early disease detection and precision medicine. In the biomarker discovery phase, it is important to capture as many candidate markers as possible in a biological sample. To meet this demand, we have developed both sandwich-based and label-based antibody array platforms for candidate biomarker screening. Currently, the expression levels of more than 1000 proteins can be quantitatively measured using our sandwich-based platform. Most proteins can be detected at pg/ml levels; an additional 2000 proteins can be captured by the label-based platform. Therefore, in total, 3000 proteins can be profiled by combining both platforms. Furthermore, potential biomarkers with well-documented importance from the literature can be collected. Additional antibody arrays can then be generated targeting those candidates, allowing better biomarkers to ultimately be optimized and identified. Finally, to translate the biomarkers to clinical applications, we have developed an automated solution to detect multiple proteins in array format. Using this platform, we have analyzed hundreds of serum samples from different diseases including hepatoma, kidney cancer, endometriosis, glioblastoma and other diseases. A number of valuable biomarker panels which show high specificity and sensitivity have been identified. The results demonstrate the great promise of our platform for identifying and developing candidate biomarkers with potential clinical significance which may be broadly applicable to cancer and other human diseases.