Application of proteomics in biological and biotechnological research

Our research enables a wide range of applications across diverse biological fields, allowing proteomics to be applied to various scientific questions, including general, physiological, environmental, and infection-related microbiology. Therefore, our methods are applied in multiple studies, for example:

Biology of infection and stress physiology

The rapid adaptation of pathogenic microorganisms to host immune defenses and new antimicrobial therapies necessitates the development of novel therapeutic strategies to combat bacterial infections. Achieving this requires a deeper understanding of the mechanisms underlying bacterial adaptation. We are involved in numerous physiological studies that use comparative protein expression analyses to provide improved qualitative insights into these adaptive networks. Some examples include:

Absolute protein quantification in systems biology

In systems biology, the generation of interdependent data requires the integration of large scale ‘omics’ studies each yielding absolute data for different levels of cellular components like DNA, RNA, proteins or metabolites. Although each single ‘omics’ level data leads to unique information, the analysis of the proteome is particularly valuable due to the nature of proteins as the real effectors of cellular metabolism (enzymes and structural determinants) throughout all kingdoms of life. For generation of absolute data in systems biology approaches we rely on three different workflows:

  1. Determination of absolute quantities of single proteins in complex mixtures by AQUA and targeted proteomics
  2. 2D Gel based absolute quantification combining AQUA and state-of-the-art 2D-PAGE
  3. Absolute quantification based on LC-MS techniques (TOP3 on data independent MS-platforms)

Environmental Metaproteomics

Fascinating biological processes occur throughout natural environments that could not be fully explored with pre-proteomics methodologies. This applies, for example, to dynamic coastal regions, marine and terrestrial soils, microbial mats, and highly complex microbiomes such as those found in the human gut or the rumen. While genomics and transcriptomics describe the potential and activity of microorganisms, metaproteomics provides access to the functional level. By analyzing proteins as the actual mediators of metabolism, we gain insight into the processes that are actively taking place within a microbial community.