Proteome2virus: Shotgun mass spectrometry data analysis pipeline for virus identification
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...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-06-01
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| Series: | Journal of Clinical Virology Plus |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2667038023000145 |
| _version_ | 1797801632409321472 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Manon Balvers |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-13T04:53:25Z |
| format | Article |
| id | doaj.art-4e3ff4238d774e60832de8aa124cc2c4 |
| institution | Directory Open Access Journal |
| issn | 2667-0380 |
| language | English |
| last_indexed | 2024-03-13T04:53:25Z |
| publishDate | 2023-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Clinical Virology Plus |
| spelling | doaj.art-4e3ff4238d774e60832de8aa124cc2c42023-06-18T05:03:57ZengElsevierJournal of Clinical Virology Plus2667-03802023-06-0132100147Proteome2virus: Shotgun mass spectrometry data analysis pipeline for virus identificationManon Balvers0Isabelle F. Gordijn1Ingrid A.I. Voskamp-Visser2Merel F.A. Schelling3Rob Schuurman4Esther Heikens5Rene Braakman6Christoph Stingl7Hans C. van Leeuwen8Theo M. Luider9Lennard J. Dekker10Evgeni Levin11Armand Paauw12HORAIZON Technology BV., Delft, the NetherlandsDepartment of CBRN Protection, Netherlands Organization for Applied Scientific Research TNO, TNO, P.O. Box 45, 2280 AA Rijswijk, Rijswijk, the NetherlandsDepartment of CBRN Protection, Netherlands Organization for Applied Scientific Research TNO, TNO, P.O. Box 45, 2280 AA Rijswijk, Rijswijk, the NetherlandsDepartment of CBRN Protection, Netherlands Organization for Applied Scientific Research TNO, TNO, P.O. Box 45, 2280 AA Rijswijk, Rijswijk, the NetherlandsDepartment of Medical Microbiology, University Medical Center Utrecht, Utrecht, the NetherlandsDepartment of Medical Microbiology, Hospital St Jansdal, Harderwijk, the NetherlandsDepartment of CBRN Protection, Netherlands Organization for Applied Scientific Research TNO, TNO, P.O. Box 45, 2280 AA Rijswijk, Rijswijk, the NetherlandsDepartment of Neurology, Erasmus MC, Rotterdam, the NetherlandsDepartment of CBRN Protection, Netherlands Organization for Applied Scientific Research TNO, TNO, P.O. Box 45, 2280 AA Rijswijk, Rijswijk, the NetherlandsDepartment of Neurology, Erasmus MC, Rotterdam, the NetherlandsDepartment of Neurology, Erasmus MC, Rotterdam, the NetherlandsHORAIZON Technology BV., Delft, the NetherlandsDepartment of CBRN Protection, Netherlands Organization for Applied Scientific Research TNO, TNO, P.O. Box 45, 2280 AA Rijswijk, Rijswijk, the Netherlands; Corresponding author.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.http://www.sciencedirect.com/science/article/pii/S2667038023000145DiagnosisMass spectrometryProteomePeptidesSARS-CoV-2Virus |
| spellingShingle | 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 Proteome2virus: Shotgun mass spectrometry data analysis pipeline for virus identification Journal of Clinical Virology Plus Diagnosis Mass spectrometry Proteome Peptides SARS-CoV-2 Virus |
| title | Proteome2virus: Shotgun mass spectrometry data analysis pipeline for virus identification |
| title_full | Proteome2virus: Shotgun mass spectrometry data analysis pipeline for virus identification |
| title_fullStr | Proteome2virus: Shotgun mass spectrometry data analysis pipeline for virus identification |
| title_full_unstemmed | Proteome2virus: Shotgun mass spectrometry data analysis pipeline for virus identification |
| title_short | Proteome2virus: Shotgun mass spectrometry data analysis pipeline for virus identification |
| title_sort | proteome2virus shotgun mass spectrometry data analysis pipeline for virus identification |
| topic | Diagnosis Mass spectrometry Proteome Peptides SARS-CoV-2 Virus |
| url | http://www.sciencedirect.com/science/article/pii/S2667038023000145 |
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