CHAPTER 4: Sample Preparation and Profiling: Biomarker Discovery in Body Fluids by Proteomics

The analysis of body fluids is challenging due to complexity of the sample and the wide dynamic concentration range of proteins and peptides. Sample preparation is a critical step to improve the overall sensitivity of the analytical methodology as well as to arrive at reproducible results. Sample preparation may affect the outcome of a study due to the introduction of changes in protein or metabolite profiles that are not related to disease but rather to sample stability. In this chapter we exemplify a number of cases related to the profiling of serum, urine, epithelial lining fluid and cerebrospinal fluid where sample preparation plays a crucial role. We further describe analytical workflows that allow fractionating proteins and peptides prior to LC-MS/MS analysis and discuss their merits and potential pitfalls.