Protein–protein interactions and protein complex/aggregate formation play an essential role in almost all biological functions and activities. Through a nanoparticle aggregation immunoassay, we discovered that some proteins are substantially more complexed/aggregated in cancer tissues than normal tissues. This study examined four biomarkers proteins, CA125, CEA (carcinoembryonic antigen), CA19-9 and PAP (prostatic acid phosphatase) in ovarian, colon and prostate tissue lysates. The most exciting results were observed from the PAP assay of prostate tissues: prostate cancer can be clearly distinguished from normal prostate and prostate with benign conditions such as BPH (benign prostate hyperplasia) based on the complex/aggregation level of PAP in prostate tissue lysates. The complex/aggregate level of a protein can be potential biomarkers for cancer detection and diagnosis.