Proteomic Analysis of Biological Fluids

Biological fluids are proteinaceous liquids or suspensions released through different body orifices or through penetration of the skin. These fluids are the result of multiple tissues and cell types and contain extensive, highly complex, and dynamic protein populations that reflect both the transcriptional program of the originating cells and a record of the individual's health status. Body fluids are readily accessible to clinicians and researchers, and as such proteomic analyses are an important component of clinical studies, fertility studies, oral health studies, and forensic investigations. Current mass spectrometry (MS) datasets have a dynamic range of up to six orders of magnitude and are as diverse as the originating tissue types. Mass spectrometry has the potential to provide information across a wide range of applications, including basic research into human biology and pathology, biochemical analysis of protein function, biomarker discovery and detection, as well as forensic investigations wherein investigators interpret a protein profile to identify the body site origin of a biological fluid. The method below describes a specimen processing workflow that is flexible in terms of biological fluid type, sample state (e.g., a dried sample extracted from evidence or neat fluid), and level of degradation. The method described here is compatible with both high sensitivity shotgun liquid chromatography-mass spectrometry LC/MS analysis and targeted (qualitative or quantitative) MS-based analysis of biomarker candidates.