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The promise of mass spectrometry-based virus proteomics: taking a peek at current bioinformatics applications and limitations

  • Driven by recent technological advances and the need for improved viral diagnostic applications, mass spectrometry-based proteomics comes into play for detecting viral pathogens accurately and efficiently. However, the lack of specific algorithms and software tools presents a major bottleneck for analyzing data from host-virus samples. For example, accurate species- and strain-level classification of a priori unidentified organisms remains a very challenging task in the setting of large search databases. Another prominent issue is that many existing solutions suffer from the protein inference issue, aggravated because many homologous proteins are present across multiple species. One of the contributing factors is that existing bioinformatic algorithms have been developed mainly for single-species proteomics applications for model organisms or human samples. In addition, a statistically sound framework was lacking to accurately assign peptide identifications to viral taxa. In thisDriven by recent technological advances and the need for improved viral diagnostic applications, mass spectrometry-based proteomics comes into play for detecting viral pathogens accurately and efficiently. However, the lack of specific algorithms and software tools presents a major bottleneck for analyzing data from host-virus samples. For example, accurate species- and strain-level classification of a priori unidentified organisms remains a very challenging task in the setting of large search databases. Another prominent issue is that many existing solutions suffer from the protein inference issue, aggravated because many homologous proteins are present across multiple species. One of the contributing factors is that existing bioinformatic algorithms have been developed mainly for single-species proteomics applications for model organisms or human samples. In addition, a statistically sound framework was lacking to accurately assign peptide identifications to viral taxa. In this presentation, an overview is given on current bioinformatics developments that aim to overcome the above-mentioned issues using algorithmic and statistical methods. The presented methods and software tools aim to provide tailored solutions for both discovery-driven and targeted proteomics for viral diagnostics and taxonomic sample profiling. Furthermore, an outlook is provided on how the bioinformatic developments might serve as a generic toolbox, which can be transferred to other research questions, such as metaproteomics for profiling microbiomes and identifying bacterial pathogens.zeige mehrzeige weniger

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Metadaten
Autor*innen:Thilo MuthORCiD
Dokumenttyp:Vortrag
Veröffentlichungsform:Präsentation
Sprache:Englisch
Jahr der Erstveröffentlichung:2022
Organisationseinheit der BAM:VP Vizepräsident
VP Vizepräsident / VP.1 eScience
DDC-Klassifikation:Naturwissenschaften und Mathematik / Chemie / Analytische Chemie
Freie Schlagwörter:Bioinformatic algorithms; Data science; Mass spectrometry; Virus detection
Themenfelder/Aktivitätsfelder der BAM:Chemie und Prozesstechnik
Veranstaltung:European Virus Bioinformatics Center in-silico lecture series
Veranstaltungsort:Online meeting
Beginndatum der Veranstaltung:28.02.2022
Verfügbarkeit des Dokuments:Datei im Netzwerk der BAM verfügbar ("Closed Access")
Datum der Freischaltung:22.12.2022
Referierte Publikation:Nein
Eingeladener Vortrag:Ja
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