Quantitative Proteomics Techniques in Biomarker Discovery

There are several important things to consider when setting up a proteomics biomarker discovery study. The methodological approach has to be chosen. In this chapter, it is of importance to consider the basic difference between bottom-up and top-down approaches. While bottom-up approaches are mainly used for biomarker discovery it still makes sense to consider top-down strategies as well. They may be used to identify disease-related changes in the expression of protein isoforms or aberrant post-translational modifications (PTMs). A technique that very recently complemented the collection of proteomics methods is mass spectrometry imaging (MSI). Matrix-assisted laser desorption ionization (MALDI) MSI enhances quantitative proteomics by an additional dimension as it considers the spatial distribution of proteins in the tissue and the correlation to histological information. Although developed almost 40 years ago, two-dimensional electrophoresis (2-DE) is still one of the methods of choice when analyzing complex protein mixtures.