MassIVE MSV000095830

Partial Public PXD055780

MSIght: A Modular Platform for Improved Confidence in Global, Untargeted Mass Spectrometry Imaging Annotation

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Description

Mass spectrometry imaging (MSI) has gained popularity in large-scale clinical analyses due to its high sensitivity, specificity and throughput. However, global profiling experiments are often still restricted to LC-MS/MS analyses that lack spatial localization due to low throughput methods for on-tissue peptide confirmation. Parallel LC-MS/MS confirmation of extracted peptides is often utilized with MALDI-MSI; however, integration and analysis of the two data sets once again presents a bottleneck in throughput. Further, the incorporation of histological stains is critical for mapping identified peptides of interest back to relevant tissue regions, yet many software generated for this are not readily accessible to those lacking coding capabilities. Here, we present a novel platform termed MSIght, which automates the integration of these multiple modalities into an accessible and modular platform. Histological stains of tissue sections are co-registered to their respective MSI data sets to improve spatial localization and resolution of identified peptides. LC-MS/MS data of extracted peptides is used to confirm putative MSI identifications and generate confident MS images in an untargeted manner. This platform enables large-scale clinical cohorts to utilize MSI for global proteomic profiling to uncover novel biomarkers in a spatial manner, thus widely expanding the utility of MSI in clinical discovery. [doi:10.25345/C5V11VX89] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: MALDI ; multimodal imaging ; mass spectrometry imaging ; histology

Contact

Principal Investigators:
(in alphabetical order) 		Lingjun Li, University of Wisconsin-Madison, United States
Submitting User: lfields
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Identification Results
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Quantification Results
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Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

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Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.