Biomarker validation remains one of the most important constraints to development of new clinical diagnostic assays. To address this challenge, an immuno-mass spectrometric assay known as SISCAPA has been developed for quantitation of protein biomarkers in human blood. The SISCAPA assay overcomes the sensitivity barrier facing most mass spectrometric approaches by utilizing high affinity antibodies for enrichment of specific surrogate peptide analytes from complex mixtures such as trypsin-digested human plasma. However, several technological barriers remain before the SISCAPA technology gains widespread use for biomarker validation. Improvements are required in areas such as selection of high affinity anti-peptide antibodies, peptide detection sensitivity and increasing sample throughput to allow biomarker validation on large sample sets. The work presented in this dissertation describes the development of new methods for antibody selection and for high-throughput application of SISCAPA technology to biomarker measurement in human plasma. Specifically, two technological developments are described: 1) an assay called MiSCREEN was developed, which allows high-throughput screening of anti-peptide antibodies, enabling selection of high affinity reagents for de novo SISCAPA assays and 2) a liquid chromatography (LC)-free SISCAPA assay was developed that enables quantitation of surrogate peptides using both MALDI-TOF and RapidFire/MS platforms. Taken together, these technological advances provide a meaningful solution to the biomarker validation dilemma and allow a unified system for biomarker qualification, verification, validation and development of clinical assays for diagnosis and monitoring of a variety of diseases. To demonstrate the utility of the unified SISCAPA system for biomarker measurement, an assay was developed for protein C inhibitor (PCI) as a marker for prediction of biochemical recurrence in prostate cancer patients. The PCI-specific analyte was shown to predict biochemical recurrence of prostate cancer after radiation/hormone treatment. Early stage detection of recurrence was achieved, when compared to the ‘gold standard’ marker for prostate cancer, prostate specific antigen (PSA). Two-dimensional gel electrophoresis studies on PCI, revealed unique protein spots in a serum sample from a biochemically recurrent patient. Studying such alterations at the protein level may enable understanding of the molecular mechanisms by which PCI is involved in prostate cancer progression. / Graduate