Complexity reduction of clinical samples for routine mass spectrometric analysis

The precise measurement of protein abundance levels in highly complex biological samples such as plasma remains challenging. The wide range of protein concentrations impairs the detection of low-abundant species and the high number of peptide components to analyze results in interferences leading to erroneous quantitative results. The advances in MS instrumentation, with improved selectivity and sensitivity, partially address these issues, but sample preparation techniques remain the pivotal element to obtain robust routine mass spectrometric assays with a low LOD. A number of methodologies have been proposed and refined over the past two decades to reduce the range of protein concentrations and the number of peptide components. Whereas most of the methods have proven their utility for discovery studies, only a few are actually applicable to routine quantitative studies. In this account, common protein- and peptide-based fractionation methods are discussed, and illustrated with practical examples, with a focus on methods suited for clinical samples scheduled for biomarker validation assays and subsequent routine clinical mass spectrometric analyses.