Sample preparation and profiling: mass-spectrometry-based profiling strategies. In Comprehensive Biomarker Discovery and Validation for Clinical Application. (Book Chapter)

In proteomics-based biomarker discovery, mass spectrometry (MS) has become an essential technology for both qualitative and quantitative analyses of proteins. In conjunction with separation methods, such as liquid chromatography (LC) or electrophoresis, the systematic peptide identification and quantification has expedited the profiling of protein components in biological samples. Numerous studies aiming at the discovery of clinically meaningful biomarker candidates have employed such MS-based proteome profiling approaches. The robustness of mass spectrometric methods has in addition facilitated large-scale analyses required for the verification and validation stages of biomarker discovery studies. In this chapter, LC-MS based profiling strategies for the discovery of protein biomarkers are discussed. In addition to reviewing the experimental strategies widely employed in the field, a specific example of biomarker discovery is discussed in this chapter.