PanHunter is a user-oriented and interactive web application allowing for in-depth data discovery across multi-omics datasets without the need for coding skills. The platform was originally built by Evotec's bioinformatics team to handle large transcriptomics datasets generated by our industrialized high-throughput transcriptomics platform. In recent years, with the advancement of high-throughput mass spectrometry-based proteomics, major advances have been made to tailor PanHunter towards handling massive datasets from different proteomics data formats.

The strength and novelty of proteomics analysis in PanHunter is founded in the holistic approach to integrate multiple levels of data (e.g. gene, protein, and post-translational modification (PTM)) through the whole workflow starting from quality control (QC) over exploratory analysis, differential expression analysis down to functional analysis, and incorporation of biological knowledge from various sources. PanHunter can map between PTM IDs, UniProt IDs, and on transcriptomics level Ensemble IDs. This mapping allows the user to analyze features simultaneously in linked plots, with data stemming from transcriptomics, proteomics or PTM data.

Here, we provide examples to highlight how the expansion of PanHunter's proteomics capabilities facilitates data integration and interpretation in the context of precision medicine, thus driving easier access to novel medicines across various therapeutic areas.

E.MPD, Evotec's molecular patient database, combining patient and omics data across multiple disease areas has been extended to cover autoimmune diseases in recent years. Integration of proteomics data from Evotecs's high-throughput mass spectrometry-based proteomics platform with patient data in PanHunter enables novel insights into the regulation of autoimmune diseases on the level of the proteome.

Evotec's ScreenPep platform allows for high-throughput screening of compounds of interest. To enable seamless data analysis after the screening, PanHunter's signature database has been broadened with proteomics signatures from Mitchell et al. 2023. These signatures can be used to investigate toxicological effects and help decipher the mechanism of action of novel compounds.

Mitchell, D.C., Kuljanin, M., Li, J. et al. A proteome-wide atlas of drug mechanism of action. Nat Biotechnol 41, 845–857 (2023). https://doi.org/10.1038/s41587-022-01539-0