Stephan Fuchs @ Robert Koch Institute (RKI) Wernigerode
The RKI is the central institution of the Federal Government in the field of disease surveillance and prevention and thus also the central institution in the field of application and measure-oriented biomedical research. The unit “Nosocomial Pathogens and Antibiotic Resistances” is dedicated to the study of bacterial pathogens with important indicator functions for the occurrence and treatment of hospital-acquired infections. We combine results from different Omics technologies and traditional molecular typing methods to answer questions regarding occurrence, transmission and risk potential of these bacteria.
We are pleased to contribute to the network by providing a de.NBI cloud-based version of our metaproteomics data analysis tool Prophane (https://www.prophane.de). Prophane enables the automated annotation of metaproteomic datasets at the level of identified proteins (or protein groups) with respect to their taxonomic origin and function. For this, results from various databases (e.g. NCBI nr, Eggnog, Pfams) and algorithms (e.g. diamond blastp, hmmscan) can be integrated. Moreover, spectrum-based quantification methods can be applied. To facilitate data interpretation, taxonomic and functional sample compositions are visualized by interactive plots. Prophane was established in 2011 and since then has been used in various studies in different fields such as molecular ecology, systems biology and microbiomics. Our activities within the de.NBI network also include workshops and practical training in metaproteomics data analysis.
The group will create, maintain and extend a web-based version of Prophane. In cooperation with the de.NBI partner project 'MetaProtServ' (Dirk Benndorf and Gunter Saake) and partners at the Hasso Plattner Institute (Bernhard Renard), a seamless and fully featured and easy-to-use workflow covering all steps of metaproteomics data analyses will be established by linking both MetaProteomeAnalyzer (MPA) and Prophane. This work is supported by the by the DFG (“Nachhaltigkeit von Forschungssoftware”).
Unit 13: Nosocomial Pathogens and Antibiotic Resistances
Robert Koch Institute (RKI)