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Viral Biomarker Detection and Validation Using MALDI Mass Spectrometry Imaging (MSI)

(1) Background: MALDI imaging is a technique that still largely depends on time of flight (TOF)-based instrument such as the Bruker UltrafleXtreme. While capable of performing targeted MS/MS, these instruments are unable to perform fragmentation while imaging a tissue section necessitating the relia...

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Autores principales: O’Rourke, Matthew B., Roediger, Ben R., Jolly, Christopher J., Crossett, Ben, Padula, Matthew P., Hansbro, Phillip M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9506211/
https://www.ncbi.nlm.nih.gov/pubmed/36136311
http://dx.doi.org/10.3390/proteomes10030033
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author O’Rourke, Matthew B.
Roediger, Ben R.
Jolly, Christopher J.
Crossett, Ben
Padula, Matthew P.
Hansbro, Phillip M.
author_facet O’Rourke, Matthew B.
Roediger, Ben R.
Jolly, Christopher J.
Crossett, Ben
Padula, Matthew P.
Hansbro, Phillip M.
author_sort O’Rourke, Matthew B.
collection PubMed
description (1) Background: MALDI imaging is a technique that still largely depends on time of flight (TOF)-based instrument such as the Bruker UltrafleXtreme. While capable of performing targeted MS/MS, these instruments are unable to perform fragmentation while imaging a tissue section necessitating the reliance of MS1 values for peptide level identifications. With this premise in mind, we have developed a hybrid bioinformatic/image-based method for the identification and validation of viral biomarkers. (2) Methods: Formalin-Fixed Paraffin-Embedded (FFPE) mouse samples were sectioned, mounted and prepared for mass spectrometry imaging using our well-established methods. Peptide identification was achieved by first extracting confident images corresponding to theoretical viral peptides. Next, those masses were used to perform a Peptide Mmass Fingerprint (PMF) searched against known viral FASTA sequences against a background mouse FASTA database. Finally, a correlational analysis was performed with imaging data to confirm pixel-by-pixel colocalization and intensity of viral peptides. (3) Results: 14 viral peptides were successfully identified with significant PMF Scores and a correlational result of >0.79 confirming the presence of the virus and distinguishing it from the background mouse proteins. (4) Conclusions: this novel approach leverages the power of mass spectrometry imaging and provides confident identifications for viral proteins without requiring MS/MS using simple MALDI Time Of Flight/Time Of Flight (TOF/TOF) instrumentation.
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spelling pubmed-95062112022-09-24 Viral Biomarker Detection and Validation Using MALDI Mass Spectrometry Imaging (MSI) O’Rourke, Matthew B. Roediger, Ben R. Jolly, Christopher J. Crossett, Ben Padula, Matthew P. Hansbro, Phillip M. Proteomes Article (1) Background: MALDI imaging is a technique that still largely depends on time of flight (TOF)-based instrument such as the Bruker UltrafleXtreme. While capable of performing targeted MS/MS, these instruments are unable to perform fragmentation while imaging a tissue section necessitating the reliance of MS1 values for peptide level identifications. With this premise in mind, we have developed a hybrid bioinformatic/image-based method for the identification and validation of viral biomarkers. (2) Methods: Formalin-Fixed Paraffin-Embedded (FFPE) mouse samples were sectioned, mounted and prepared for mass spectrometry imaging using our well-established methods. Peptide identification was achieved by first extracting confident images corresponding to theoretical viral peptides. Next, those masses were used to perform a Peptide Mmass Fingerprint (PMF) searched against known viral FASTA sequences against a background mouse FASTA database. Finally, a correlational analysis was performed with imaging data to confirm pixel-by-pixel colocalization and intensity of viral peptides. (3) Results: 14 viral peptides were successfully identified with significant PMF Scores and a correlational result of >0.79 confirming the presence of the virus and distinguishing it from the background mouse proteins. (4) Conclusions: this novel approach leverages the power of mass spectrometry imaging and provides confident identifications for viral proteins without requiring MS/MS using simple MALDI Time Of Flight/Time Of Flight (TOF/TOF) instrumentation. MDPI 2022-09-13 /pmc/articles/PMC9506211/ /pubmed/36136311 http://dx.doi.org/10.3390/proteomes10030033 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
O’Rourke, Matthew B.
Roediger, Ben R.
Jolly, Christopher J.
Crossett, Ben
Padula, Matthew P.
Hansbro, Phillip M.
Viral Biomarker Detection and Validation Using MALDI Mass Spectrometry Imaging (MSI)
title Viral Biomarker Detection and Validation Using MALDI Mass Spectrometry Imaging (MSI)
title_full Viral Biomarker Detection and Validation Using MALDI Mass Spectrometry Imaging (MSI)
title_fullStr Viral Biomarker Detection and Validation Using MALDI Mass Spectrometry Imaging (MSI)
title_full_unstemmed Viral Biomarker Detection and Validation Using MALDI Mass Spectrometry Imaging (MSI)
title_short Viral Biomarker Detection and Validation Using MALDI Mass Spectrometry Imaging (MSI)
title_sort viral biomarker detection and validation using maldi mass spectrometry imaging (msi)
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9506211/
https://www.ncbi.nlm.nih.gov/pubmed/36136311
http://dx.doi.org/10.3390/proteomes10030033
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