Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Untargeted Spatial Metabolomics and Spatial Proteomics on the Same Rat Brain Tissue Section

ABSTRACT: Proteomic data from rat brain. Replicate samples were analyzed via the microPOTS platform.

INSTRUMENT(S): timsTOF SCP

ORGANISM(S): Rattus Norvegicus (ncbitaxon:10116)

SUBMITTER: Christopher Anderton

PROVIDER: MSV000095665 | MassIVE | Tue Aug 20 18:56:00 BST 2024

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

GNPS - Untargeted Spatial Metabolomics and Spatial Proteomics on the Same Rat Brain Tissue Section

Project description:Proteomic data from rat brain. Replicate samples were analyzed via the microPOTS platform.

2024-08-20 | MSV000095665 | GNPS

Spatial Multimodal Analysis: MALDI-MSI and Spatial Transcriptomics within the same tissue section

Project description:We present a spatial omics approach that merges and expands the capabilities of independently performedin situassays on a single tissue section. Our spatial multimodal analysis combines histology, mass spectrometry imaging, and spatial transcriptomics to facilitate precise measurements of mRNA transcripts and low-molecular weight metabolites across tissue regions. We demonstrate the potential of our method using murine and human brain samples in the context of dopamine and Parkinson’s disease.

2023-05-21 | GSE232910 | GEO

Enabling spatial metabolomics and spatial proteomics from the same tissue section

Project description:We developed a workflow for comprehensive multi-omics profiling from a single tissue section (STS) using different mass spectrometry (MS)-modalities. We addressed key challenges associated with the need for serial sections and substrate incompatibilities between the modalities. We enhanced the functionality of an insulative substrate by employing metal-assisted approach, enabling its integration into dual applications for metabolite and proteomics imaging from STS using complementary MS-techniques. This allows for metabolite imaging using matrix-assisted laser desorption/ionization-MS imaging (MALDI-MSI) while preserving its compatibility for subsequent proteome profiling with laser capture microdissection (LCM)-based MS technology. Peptides were identified using DIA-NN.

2025-08-05 | MSV000098730 | MassIVE

Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus

Project description:DBiTplus utilizes in situ reverse transcription, in-tissue delivery of DNA oligos for spatial barcoding, and RNaseH-mediated selective cDNA retrieval, preserving tissue architecture to enable highly multiplexed protein imaging and spatial transcriptomics on the same slide. Computational pipelines seamlessly integrates these modalities, allowing imaging-guided deconvolution to generate genome-scale, single-cell-resolved spatial transcriptome atlases. DBiTplus was demonstrated across diverse samples including mouse embryos, normal human lymph nodes, and formalin-fixed paraffin-embedded (FFPE) human lymphoma tissues, highlighting its compatibility with challenging clinical specimens. Applying DBiTplus to human lymphoma samples reveals key mechanisms driving lymphomagenesis, progression, and notably, the progression of indolent marginal zone lymphoma (MZL) or the transformation from chronic lymphocytic leukemia (CLL) to diffuse large B-cell lymphoma (DLBCL), including uniquely, the spatially resolved involvement of microRNAs in modulating the transformation dynamics. Thus, DBiTplus is a unified workflow including integrative experimental procedure and computational innovation for spatially resolved single-cell atlasing and exploration of biological pathways cell-by-cell at genome-scale.

2025-10-04 | GSE308167 | GEO

Spatial Multimodal Analysis: MALDI-MSI and Spatial Transcriptomics within the same tissue section

Project description:Spatial Multimodal Analysis: MALDI-MSI and Spatial Transcriptomics within the same tissue section

| PRJNA974409 | ENA

Integrated Mass Spectrometry Imaging and Omics Workflows on the Same Tissue Section Using Parafilm-Assisted Microdissection

Project description:In this work, we demonstrate the use of grid-aided, parafilm-assisted microdissection to perform MALDI MS imaging and shotgun proteomics and metabolomics in a combined workflow and using only a single tissue section. The grid is generated by microspotting of acid dye 25 using a piezoelectric microspotter. In the gas phase, the dye is detectable as a free radical species, and its distribution can be superimposed with ion images generated by tissue components, then used as a guide to locate regions of interest and aid during manual microdissection. Subjecting the dissected pieces to the modified Folch method allows to separate the metabolic components from the proteins. The proteins can then be subjected to overnight digestion under controlled conditions to improve protein identification yields. The proof of concept experiment on rat brain generated 162 and 140 metabolite assignments from three ROIs (cerebellum, hippocampus and midbrain/hypothalamus) in positive and negative mode, respectively, and 890, 1,303 and 1,059 unique protein accessions. Integrated metabolite and protein overrepresentation analysis identified pathways associated with the biological functions of each ROI, most of which were not identified when looking at the protein and metabolite lists individually. This combined MALDI MS imaging and multi-omics approach benefits from the advantages of both methods (molecular mapping from MSI and increased depth of coverage from shotgun proteomics and metabolomics), and further extends the amount of information that can be generated from single tissue sections.

2017-03-20 | PXD005345 | Pride

RaMALDI: Enabling simultaneous Raman and MALDI imaging of the same tissue section.

Project description:Multimodal tissue imaging techniques that integrate two complementary modalities are powerful discovery tools for unraveling biological processes and identifying biomarkers of disease. Combining Raman spectroscopic imaging (RSI) and matrix-assisted laser-desorption/ionization (MALDI) mass spectrometry imaging (MSI) to obtain fused images with the advantages of both modalities has the potential of providing spatially resolved, sensitive, specific biomolecular information, but has so far involved two separate sample preparations, or even consecutive tissue sections for RSI and MALDI MSI, resulting in images with inherent disparities. We have developed RaMALDI, a streamlined, integrated, multimodal imaging workflow of RSI and MALDI MSI, performed on a single tissue section with one sample preparation protocol. We show that RaMALDI imaging of various tissues effectively integrates molecular information acquired from both RSI and MALDI MSI of the same sample, which will drive discoveries in cell biology, biomedicine, and pathology, and advance tissue diagnostics.

| S-EPMC10544780 | biostudies-literature

Murine Rat Brain Injury

Project description:Murine Rat Brain Injury

| PRJNA91203 | ENA

In situ tissue profile of rat trigeminal nerve in trigeminal neuralgia using spatial transcriptome sequencing

Project description:Investigation on the transcriptome and intercellular communication of different cells of trigeminal nerve in trigeminal neuralgia rat by spatial transcriptome sequencing

2024-02-29 | GSE233838 | GEO

Rat Adipose Tissue

Project description:Male 130 day old rat adipose tissue from control and obese rats Keywords: ordered

2004-11-30 | GSE1813 | GEO