Title
Proteome2virus: Shotgun mass spectrometry data analysis pipeline for virus identification
Author
Balvers, M.
Gordijn, I.F.
Voskamp-Visser, A.I.
Schelling M.F.A.,
Schuurman, R.
Heikens, E.
Braakman, R.
Stingl, C.
van Leeuwen, H.C.
Luider, T.M.
Dekker, L.J.
Levin, E.
Paauw, A.
Publication year
2023
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.
Subject
Diagnosis
Mass spectrometry
Proteome
Peptides
SARS-CoV-2
Virus
To reference this document use:
http://resolver.tudelft.nl/uuid:78cecb52-31db-4453-992f-aae812373030
DOI
https://doi.org/10.1016/j.jcvp.2023.100147
TNO identifier
985395
Publisher
Elsevier
Source
Journal of Clinical Virology Plus, 3 (3), 100147
Document type
article