Serving your proteomics analysis needs – the Core Unit for Bioinformatics (CUBiMed.RUB) in Bochum and de.NBI 2.0 / ELIXIR-DE

Background: As a recently established core unit within the Medical Faculty of the Ruhr-University Bochum we are succeeding the Service Center "Bioinformatics for Proteomics - BioInfra.Prot" of the "German Network for Bioinformatic Infrastructure (de.NBI)", which was a seven year-BMBF funded project ending December 2021. Since March 2024 there is additionally a continued BMBF funding (de.NBI 2.0) via the "Forschungszentrum Jülich", which realizes the German node ELIXIR-DE of the European ELIXIR infrastructure. We provide a comprehensive portfolio of Bioinformatics cooperation and infrastructure possibilities to clinical, biological, and mass spectrometry users.

Materials and Methods: On the one hand we provide well-established tools and workflows for the analysis of mass spectrometry data regarding peptide identification, protein inference and peptide-to-protein quantification, as well as finding protein variants. On the other hand, we provide univariate and multivariate statistical methodology such as t-tests, multi-group tests, clustering and classification / machine learning. This portfolio is provided by web services / github projects, but also as Bioinformatics and Biostatistical consulting or even analysis (free for academic cooperation partners). All topics are also covered in training and education activities.

Results: Bioinformatics tools for Proteomics such as a quality control workflow, PIA (Protein Inference Algorithm), CalibraCurve or MaCPepDB (Mass Centric Peptide Database) have been developed, are maintained, and will be extended by user needs. Virtual servers and docker containers can be started by users in a high-core and / or high-RAM cloud infrastructure. Clustering, classification with machine learning and even deep learning are applied to Proteomics data and can be discussed with interested researchers. Training courses, including both beginner and expert R courses, are held regularly. The Proteomics cooperation possibilities are complemented by a multi-omics department of the core unit, that can also work with proteogenomics data.

Conclusion: By providing free, high-quality infrastructure and cooperation opportunities, we play a significant role in the bioinformatics infrastructure within the proteomics research landscape. With that we complement the existing mass spectrometry core facilities in Germany and Europe.