M. Eisenacher, Ruhr University Bochum
Service center: Service center Bioinformatics for Proteomics – BioInfra.Prot
The pandemic of COVID-19 caused by the virus SARS-CoV-2 has an enormous negative impact on all affected health systems, economies and societies. Thus, to alleviate and overcome the negative consequences as fast as possible it is crucial to focus extensive research efforts on the development of effective test methods for infection, drugs and vaccines. To this end, worldwide collaboration of interdisciplinary researchers and experts involved in COVID-19-related research and efficient sharing of high-quality data and results are needed to accelerate this endeavor.
Public repositories for microbiological data such as the PRIDE archive for mass spectrometry-based proteomics data, which is part of the ProteomeXchange Consortium, are extremely important infrastructures, which enable the provision of SARS-CoV-2-related datasets to all researchers worldwide. PRIDE ensures that the published data has a high quality, is stored in standard data formats and that all metadata and information needed for reanalysis is available. Moreover, PRIDE provides a highly performant technical infrastructure that facilitates efficient data transfer, findability, accessibility and security.
In close collaboration with the PRIDE team at EMBL-EBI headed by Juan Antonio Vizcaíno, BioInfra.Prot staff members are involved in the curation of PRIDE uploads and corresponding user consulting. Currently, Bioinfra.Prot staff members have processed various different SARS-CoV-2-related proteomics datasets, whereas some of them are already publicly available in PRIDE (e.g., PXD018760). These can be downloaded and reanalyzed by anyone in the context of any research project. Thus, online data infrastructures such as the ELIXIR core data resource PRIDE and BioInfra.Prot contribute to the acceleration of international COVID-19-related research efforts.
For further information on data available in PRIDE: https://www.ebi.ac.uk/pride/