Size matters: Miniaturised interaction proteomics with ultra-low input requirements

Cellular activities are dictated by proteins. Deciphering how proteins interact in a healthy or diseased state is a key area of interest in biology. Eventually, this will facilitate the development of drugs for many diseases including cancer, which is ultimately the result of misregulated protein homeostasis.

In recent years, affinity purification coupled to mass spectrometry (AP-MS) has been the preferred method to identify cellular protein-protein interactions. Unfortunately, AP-MS experiments typically require large amounts (millions of cells) of input material. For this reason, AP-MS studies are mostly restricted to cancer cell lines that can be grown in large quantities in vitro. Cristina Furlan and René Dirks from the groups of Michiel Vermeulen and Hendrik Marks, research theme Cancer development and immune defense, teamed up to address these limitations by developing a low input AP-MS workflow, called on-chip AP-MS, which can be used to perform AP-MS experiments using a few micrograms of lysate from a few thousand cells. This was achieved by implementing an AP-MS method in a automated, microfluidic device from the company Fluidigm using nanoliter volumes.

With the development of on-chip AP-MS, clinical samples, rare cell types and organoids, which are difficult to obtain in large quantities, can now be investigated using interaction proteomics studies. The field of mass spectrometry-based interaction proteomics is thus taking an important next step towards applications in biology and medicine which thus far, due to technical constraints, have remained elusive. This study was recently published in Nature Communications.