Proteome2virus: Shotgun mass spectrometry data analysis pipeline for virus identification

Manon Balvers, Isabelle F. Gordijn, Ingrid A.I. Voskamp-Visser, Merel F.A. Schelling, Rob Schuurman, Esther Heikens, Rene Braakman, Christoph Stingl, Hans C. van Leeuwen, Theo M. Luider, Lennard J. Dekker, Evgeni Levin, Armand Paauw*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

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Abstract

Objectives: Shotgun proteomics is a generic method enabling detection of multiple viral species in one assay. The reliable and accurate identification of these viral species by analyzing peptides from MS-spectra is a challenging task. The aim of this study was to develop an easy accessible proteome analysis approach for the identification of viruses that cause respiratory and gastrointestinal infections. Methods: For this purpose, a shotgun proteomics based method and a web application, ‘proteome2virus’, were developed. Identified peptides were searched in a database comprising proteomic data of 46 viruses known to be infectious to humans. Results: The method was successfully tested for cultured viruses and eight fecal samples consisting of ten different viral species from seven different virus families, including SARS-CoV-2. The samples were prepared with two different sample preparation methods and were measured with two different mass spectrometers. Conclusions: The results demonstrate that the developed web application is applicable to different MS data sets, generated from two different instruments, and that with this approach a high variety of clinically relevant viral species can be identified. This emphasizes the potential and feasibility for the diagnosis of a wide range of viruses in clinical samples with a single shotgun proteomics analysis.

Original languageEnglish
Article number100147
JournalJournal of Clinical Virology Plus
Volume3
Issue number2
DOIs
Publication statusPublished - Jun 2023

Bibliographical note

Funding Information:
This work was supported by the Dutch Ministry of Defence [grant number V2207] and by the Dutch Ministry of Economic Affairs through the Early Research Program funded project Pandemic Preparedness. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Publisher Copyright:
© 2023

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