This article is sponsored by Evotec.
To enable Evotec’s precision medicine approach, we have been building technology platforms that allow PanOmics or multi-omics data generation at an industrialised scale. The technologies cover the whole range of biomolecules from genes to protein to metabolites. While we are using standard commercially available processes for genomics, we have invested massively into high-throughput and high-resolution transcriptomics, proteomics, and metabolomics methods. These methods allow us to study diseases processes on all molecular levels and yield a deeper understanding of the disease mechanisms and discovery of novel predictive biomarkers.
As one key element for PanOmics-driven drug discovery we have established leading high-throughput and high-resolution transcriptomics data generation capabilities. Transcriptomics, an unbiased approach to quantify mRNAs in a sample, is an excellent method to generate highly multidimensional functional readouts from biological material, thus giving a precise view on the state of cells and organs, while being highly scalable and economical. Using classical bulk (deep) RNA-Seq on thousands of human blood and tissue samples, Evotec has been building a high-quality molecular patient database – E.MPD.
Our flagship asset, the proprietary and massively scalable 384 well based ScreenSeq bulk RNA-Seq protocol, has generated more than a million high quality transcriptomes, supported drug screening and profiling campaigns, as well as toxicogenomics by providing reliable highly multidimensional readouts.
Proteomics is a rapidly evolving field that is transforming our understanding of biological systems and disease mechanisms. With the ability to analyse thousands of proteins simultaneously, proteomics empowers scientists to reveal previously unknown protein interactions, pathways, and drug targets. However, in-depth analysis of proteomics data can be challenging; it requires powerful computational tools and strong scientific expertise. This requirement is met by technology from Evotec, a life sciences company that continually leads the way in proteomic research; with its PanOmics approach, Evotec seamlessly combines both data generation and analysis.
Evotec’s data generation platform ScreenPep is among the largest mass spectrometry-based proteomics and metabolomics facilities worldwide. With over 15 years of experience in driving drug discovery with mass spectrometry-based proteomics, Evotec provides highly optimised and robust experimental strategies that can be easily tailored to different projects’ needs.
One of the key advantages of ScreenPep is being able to benefit from high throughput without compromising coverage and accuracy. ScreenPep enables the analysis of several hundred samples at an unprecedented speed and depth, detecting beyond 10,000 proteins from cells or tissues and over 4,000 proteins from human biofluid samples such as plasma.
Originally developed for screening compounds during drug discovery programmes, ScreenPep has recently been optimised for global proteomics studies from multicentric patient cohorts. High sensitivity and accuracy are achieved by combining high-end mass spectrometry instrumentation with appropriate sample preparation and data acquisition methods, spanning from nanoparticle-based protein enrichment to data-independent acquisition. Furthermore, it can detect and quantify different protein isoforms as well as their post-translational modifications (e.g., phosphorylations or ubiquitinations).
The analysis of such rich proteomic datasets is supported by Evotec’s data analysis platform – PanHunter. PanHunter is a web-based solution that was launched as a Software-as-a-Service (SaaS) product in 2022. It offers several key features that strengthen and facilitate the collaboration of large teams.
PanHunter’s highly flexible and interactive user interface enables researchers to easily explore, visualise, and analyse their own data with desired parameters.
All statistical algorithms in PanHunter are peer-reviewed, ensuring that the results are trustworthy and reproducible by users with all levels of bioinformatic skills. Specific analyses and modules can also be easily extended according to additional scientific needs. The software connects multiple omics technologies and data sources, supporting the joint analysis of not only proteomics, but also genomics, transcriptomics, metabolomics, and even clinical data. It constructs a holistic and integrated vision, enabling true understanding of complex biological systems.
Consolidating comprehensive metadata from various databases, bringing molecular and functional information, interaction networks, disease and drug signatures, biological pathways, and so on to the users. This eliminates the need to seek relevant information from multiple webpages and to upload user’s sensitive data to public domains.
In summary, by leveraging both platforms, Evotec is connecting the dots from peptide, protein, and PTM to public and proprietary knowledge, enabling true understanding of disease mechanisms at the molecular level, thus improving the probability of success and advancing drug discovery.
