Deep Proteome Profiling of Primary Skin Fibroblasts

Skin-derived primary cells and skin tissue are prime model systems to study molecular disease mechanisms on cell and tissue level. Cells and tissue can be cultivated ex vivo and protocols for both, simple 2D as well as 3D in vitro cultures reflecting different levels of complexity exist. Mass spectrometry (MS)-based proteomics is a prime approach to link molecular mechanisms to observable disease phenotypes. In this chapter, we describe in detail the analysis of 2D and 3D primary skin fibroblast cultures by MS. We focus on automated sample processing to increase throughput and usage of limited cell numbers to reduce costs. The described workflow supports the study of proteome regulation in large scale screening approaches, be it for drug discovery or in clinical studies.