Dataset Information

Viral biomarker detection and validation using MALDI Mass Spectrometry Imaging (MSI)

ABSTRACT: INTRODUCTION: Mass Spectrometry Imaging (MSI) is a hybrid mass spectrometry technique that integrates aspects of traditional microscopy and mass spectrometry-based omics analysis. The traditional MALDI TOF/TOF instrument still remains the dominant platform for this type of anal-ysis. However, with reduced mass resolution compared to other platforms it is insufficient to rely on mass resolution alone for peptide identification. Here we propose a hybrid method of data analysis that integrates both image-based analysis and a parallel protein identification workflow using peptide mass fingerprinting, and its successful application to the detection and validation of viral biomarkers. METHODS: FFPE samples were imaged as described previously in an UltrafleXtreme MALDI TOF/TOF. Total mass spectra were exported and searched against the mouse FASTA da-tabase, while companion images were exported and processed with image J. RESULTS: Peptide mass fingerprinting (PMF) revealed 14 target peptides that were successfully assigned to viral proteins while a pixel based correlational analysis revealed a very high R2 correlation (>0.81) be-tween those same peptides assigned to the NS1 and VP1 viral proteins. CONCLUSIONS: We successfully identified and validated the presence of viral biomarkers to a high degree of confidence using MALDI MSI.

INSTRUMENT(S): ultraflex

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Kidney

SUBMITTER: Matthew O'Rourke

LAB HEAD: Phil P Hansbro

PROVIDER: PXD034851 | Pride | 2022-10-13

REPOSITORIES: Pride

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Publications

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

O'Rourke Matthew B MB Roediger Ben R BR Jolly Christopher J CJ Crossett Ben B Padula Matthew P MP Hansbro Phillip M PM

Proteomes 20220913 3

(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. ( ...[more]

PMID: 36136311

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Project description:Chronic infections by hepatitis B virus (HBV) and hepatitis C virus (HCV) appear to be the most significant causes of hepatocellular carcinoma (HCC). Aberrant promoter methylation is known to be deeply involved in cancer, including HCC. In this study, we analyzed aberrant promoter methylation on genome-wide scale in 6 HCCs including 3 HBV-related and 3 HCV-related HCCs, 6 matched noncancerous liver tissues and 3 normal liver tissues by methylated DNA immunoprecipitation-on-chip analysis. Candidate genes with promoter methylation were detected more frequently in HCV-related HCC. Candidate genes methylated preferentially to HBV-related or HCV-related HCCs were detected and selected, and methylation levels of the selected genes were validated using 125 liver tissue samples, including 61 HCCs (28 HBV-related HCCs and 33 HCV-related HCCs) and matched 59 matched noncancerous livers, and 5 normal livers, by quantitative methylation analysis using MALDI-TOF mass spectrometry. Among analyzed genes, preferential methylation in HBV-related HCC was validated in 1 gene only. However, 15 genes were found methylated preferentially in HCV-related HCC, which was independent from age. Hierarchical clustering of HCC using these 15 genes stratified HCV-related HCC as a cluster of frequently methylated samples. The 15 genes included genes inhibitory to cancer-related signaling such as RAS/RAF/ERK and Wnt/b-catenin pathways. It was indicated that genes methylated preferentially in HCV-related HCC exist, and it was suggested that DNA methylation might play an important role in HCV-related HCC by silencing cancer-related pathway inhibitors. we analyzed aberrant promoter methylation in 6 HCC clinical samples (including 3 HBV-related HCCs and 3 HCV-related HCCs) and their matched noncancerous tissues on genome-wide scale by the method. Candidate regions of promoter methylation preferentially to HBV-related HCC and HCV-related HCC were selected, and the methylation levels of these genes were measured quantitatively using MALDI-TOF mass spectrometry. Expression levels of these 6 pairs of HCC and 4 more pairs of HCCs and surrounding noncancerous tissues were analyzed by expression array and are reported in this Series. <br><br>This experiment was reloaded in November 2010 after additional curation. this dataset is part of the TransQST collection.

Dataset Information

Viral biomarker detection and validation using MALDI Mass Spectrometry Imaging (MSI)

Publications

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

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