(37c) Human Fluid Sample Pretreatment for Biomarker Discovery

Human fluids – including plasma, serum, and cerebrospinal and pleural effusion fluids -- potentially are rich sources of protein biomarkers that can be used to indicate the presence or progression of disease or the response of disease to treatment regimens. Human fluids are enormously complex, with hundreds of thousands of different proteins, protein fragments and post-translational modifications that are present with concentrations that span ten orders of magnitude. Potential biomarkers are expected to be present at very low concentrations when compared with the abundant proteins, and the wide protein dynamic range far exceeds that of the analytical instrumentation used for the analysis, whether gel electrophoresis (such as DIGE) or bottom-up proteomic methods are used.

Nine protein biomarker panels have been introduced to date, but discovery of new ones has slowed considerably. We believe that one reason is that pretreatment methods applied to human fluid samples are inadequate. We review the extensive work described in the literature, and introduce new ones that we are developing at Sonata Biosciences. A particular emphasis is placed on treatment of the large volumes that are required to delve deeply into the proteome to uncover dilute protein biomarkers.