Experimental Design in Proteomic Mass Spectrometry Studies for Biomarker Discovery

Proteomics plays a crucial role in advancing our understanding of the interplay of proteins within complex biological systems. The high-dimensional data, derived at great expense, can hold very little value if careful attention is not paid to the experimental design and analysis. The use of established experimental design procedures and the incorporation of quality control can considerably increase the quality, reliability, and interpretability of the obtained results. This chapter highlights the importance of thoughtful and systematic experimental design in a proteomic mass spectrometry study and provides a comprehensive overview of the strategies to design a proteomic study.