Proteome2virus: Shotgun mass spectrometry data analysis pipeline for virus identification
Journal of Clinical Virology Plus
; 3(2) (no pagination), 2023.
Artículo
en Inglés
| EMBASE | ID: covidwho-2291858
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. Method(s) 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. Result(s) 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. Conclusion(s) 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.Copyright © 2023
Diagnosis; Mass spectrometry; Peptides; Proteome; SARS-CoV-2; Virus; article; Human coronavirus 229E; Human coronavirus OC43; Human mastadenovirus F; Human metapneumovirus; Human respiratory syncytial virus; Influenza A virus (H1N1); Influenza A virus (H3N2); Mamastrovirus; nonhuman; Norwalk virus; proteomics; real time polymerase chain reaction; Rotavirus A; Severe acute respiratory syndrome coronavirus 2; virus culture; virus identification; virus strain; proteome/ec [Endogenous Compound]; shotgun mass spectrometry
Texto completo:
Disponible
Colección:
Bases de datos de organismos internacionales
Base de datos:
EMBASE
Idioma:
Inglés
Revista:
Journal of Clinical Virology Plus
Año:
2023
Tipo del documento:
Artículo
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