TY - JOUR
T1 - Proteome2virus
T2 - Shotgun mass spectrometry data analysis pipeline for virus identification
AU - Balvers, Manon
AU - Gordijn, Isabelle F.
AU - Voskamp-Visser, Ingrid A.I.
AU - Schelling, Merel F.A.
AU - Schuurman, Rob
AU - Heikens, Esther
AU - Braakman, Rene
AU - Stingl, Christoph
AU - van Leeuwen, Hans C.
AU - Luider, Theo M.
AU - Dekker, Lennard J.
AU - Levin, Evgeni
AU - Paauw, Armand
N1 - Publisher Copyright:
© 2023
PY - 2023/6
Y1 - 2023/6
N2 - 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.
AB - 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.
KW - Diagnosis
KW - Mass spectrometry
KW - Peptides
KW - Proteome
KW - SARS-CoV-2
KW - Virus
UR - http://www.scopus.com/inward/record.url?scp=85151618645&partnerID=8YFLogxK
U2 - 10.1016/j.jcvp.2023.100147
DO - 10.1016/j.jcvp.2023.100147
M3 - Article
AN - SCOPUS:85151618645
VL - 3
JO - Journal of Clinical Virology Plus
JF - Journal of Clinical Virology Plus
IS - 2
M1 - 100147
ER -