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

doi:10.1016/j.jcvp.2023.100147

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

Neurology

Research output: Contribution to journal › Article › Academic › peer-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 language	English
Article number	100147
Journal	Journal of Clinical Virology Plus
Volume	3
Issue number	2
DOIs	https://doi.org/10.1016/j.jcvp.2023.100147
Publication status	Published - 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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Proteome2virus Shotgun mass spectrometry data analysis pipeline for virus identificationFinal published version, 1.05 MBLicence: CC BY-NC-ND

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Balvers, M., Gordijn, I. F., Voskamp-Visser, I. 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. (2023). Proteome2virus: Shotgun mass spectrometry data analysis pipeline for virus identification. Journal of Clinical Virology Plus, 3(2), Article 100147. https://doi.org/10.1016/j.jcvp.2023.100147

@article{c8abb48e25a647799454bbaf5e2d31a4,

title = "Proteome2virus: Shotgun mass spectrometry data analysis pipeline for virus identification",

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, {\textquoteleft}proteome2virus{\textquoteright}, 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.",

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

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: {\textcopyright} 2023",

year = "2023",

month = jun,

doi = "10.1016/j.jcvp.2023.100147",

language = "English",

volume = "3",

journal = "Journal of Clinical Virology Plus",

issn = "2667-0380",

publisher = "Elsevier Ltd.",

number = "2",

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Balvers, M, Gordijn, IF, Voskamp-Visser, IAI, Schelling, MFA, Schuurman, R, Heikens, E, Braakman, R, Stingl, C, van Leeuwen, HC, Luider, TM, Dekker, LJ, Levin, E & Paauw, A 2023, 'Proteome2virus: Shotgun mass spectrometry data analysis pipeline for virus identification', Journal of Clinical Virology Plus, vol. 3, no. 2, 100147. https://doi.org/10.1016/j.jcvp.2023.100147

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 - 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

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.

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U2 - 10.1016/j.jcvp.2023.100147

DO - 10.1016/j.jcvp.2023.100147

M3 - Article

AN - SCOPUS:85151618645

SN - 2667-0380

VL - 3

JO - Journal of Clinical Virology Plus

JF - Journal of Clinical Virology Plus

IS - 2

M1 - 100147

ER -

Proteome2virus: Shotgun mass spectrometry data analysis pipeline for virus identification

Abstract

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