CHAPTER 4: Sample Preparation and Profiling: Biomarker Discovery in Body Fluids by Proteomics
Published:10 Jun 2013
N. Govorukhina and R. Bischoff, in Comprehensive Biomarker Discovery and Validation for Clinical Application, ed. P. Horvatovich and R. Bischoff, The Royal Society of Chemistry, 2013, pp. 113-135.
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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.