ViPPip: A computational proteomics pipeline for virus pathogen detection and taxon-functional profiling

• Applicant: Privatdozent Dr. Thilo Muth
• Subject Area: Bioinformatics and Theoretical Biology
• Term: since 2020
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 439719438

Recent technological advances in mass spectrometry-based proteomics provide promising discovery-driven and targeted methods for detecting viral pathogens in accurate and efficient manner. A major bottleneck, however, presents the lack of specific algorithms and software tools for analyzing data from host-virus samples. For example, existing solutions for designing targeted proteomic assays neglect the issue of homologous proteins across multiple species and peptide selection algorithms are only available for model organisms or human samples.The main objective of this project is to design, prototype, implement, evaluate, document, and distribute algorithms and software modules to provide tailored solutions in proteomics for viral diagnostics that also include taxonomic and functional sample profiling. The idea of using unique marker sequences across species boundaries is used for designing an automated species-specific peptide selection algorithm in targeted assays. Further, a combined algorithmic strategy makes use of k-mer indexing and short de novo sequence tags with the goal of achieving robust mutation-tolerant classification of viral species. In addition, the concept of integrating proteomic and genomic database resources to increase the identification yield is exploited in a multi-stage, host- and virus-related search workflow. Finally, data models, metrics, statistical assessment and visualization strategies are elaborated for taxonomic and functional analysis.The outcome of this innovative project is two-fold: first, the developed algorithms will provide adapted solutions for conducting accurate viral diagnostics using unbiased search strategies and targeted assays. Second, the developed bioinformatic pipeline will serve as a generic toolbox, which can be transferred to other research questions, such as bacterial pathogen identification and profiling of microbial communities.

• DFG Programme: Research Grants