Every living being is constantly confronted with a multitude of pathogens – viruses, bacteria, fungi and other uni- and multicellular parasites – and thus requires mechanisms to defend the body from these threats. The entity of cells dealing with these threats is known as the immune system. The different cells within the immune system fulfil very distinct tasks and collaborate with each other to help the body deal with dangers from the outside and inside. The high degree of specialisation is reflected by a myriad of different immune cell phenotypes and characteristics which can rapidly change upon stimuli caused by pathogens or out-of-control host cells.
There are databases available that try to comprehensively map the expression pattern of the different immune cell types , however, these databases only contain transcriptome data and thus do not reflect the true proteomic composition of these cells. On the other hand, existing proteome databases are not specific enough as they do not account for the differences between distinct immunological cell subsets [2, 3].
We will thus expand our already existing Encyclopedia of Protein Dynamics with different proteomes of directly ex vivo derived immune cells as well as model immune cell subsets cultured in vitro. Apart from gathering information about abundance levels of different proteins across several immunological subsets to define immune cell identities via their unique proteome composition we will also focus on the effects of metabolics stress on these cells: Many immune cells have to adjust their metabolic rates as part of their differentiation process or effector function and need to deal with varying nutrient conditions in different tissues.
Another focus is the analysis of protein complexes in these cells. Little is known about the different transcription factor complexes within the different immunological subsets and how these protein complexes serve as key determinants of immune cell fate. These fate decisions can furthermore be very plastic, i.e. immune cells are able to switch between different subsets as a response to external stimuli. Multimeric receptor complexes on the cell surface relay these stimuli into the cell and thus also play a key part in the different aspects of immune cell biology. While surface markers for these different receptors and surface proteins are routinely used to characterise immune cells we do still only know little about their abundances and how the different receptors complexes are formed. We hope that our openly available and user-friendly database and visualisation tools will provide fellow researchers with invaluable tools to help understand the different aspects of immunology and thus help accelerate research in this field.