Abstract: The present invention provides methods for diagnosing cancers, such as prostate cancer. Also, methods for evaluating the prostate cancer state of a patient are described herein. These methods involve the detection, analysis, and classification of biological patterns in biological samples. The biological patterns are obtained using, for example, mass spectrometry systems, antibody based techniques, or nucleic acid based techniques. The present invention also includes therapeutic and prophylactic agents that target the biomarkers described herein. Also, the present invention provides methods for the treatment of prostate cancer using the markers described herein or agents that mimic the properties of these markers.

Abstract: Systems for customization of assays. The method includes steps of collecting case samples representing a clinical phenotypic state and control samples representing patients without said clinical phenotypic state. Preferably the system uses a mass spectrometry platform system to identify patterns of polypeptides in said case samples and in the control samples without regard to the specific identity of at least some of said polypeptides. Based on identified representative patterns of the state, the system performs optimized assays for greater sensitivity, specificity, and/or cost effectiveness.