Metabolic insights into animal-associated microbiomes with correlative spatial metabolomics and transcriptomics
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB56461 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR10314453_1.fastq.gz | Fastqsanger.gz | |||
| ERR10314453_2.fastq.gz | Fastqsanger.gz | |||
| ERR10314454_1.fastq.gz | Fastqsanger.gz | |||
| ERR10314454_2.fastq.gz | Fastqsanger.gz | |||
| ERR10314455_1.fastq.gz | Fastqsanger.gz |
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Project description:MALDI-imaging-guided Transcriptomics
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Project description:The E4 allele of Apolipoprotein E (APOE) is associated with both metabolic dysfunction and a heightened pro-inflammatory response – two findings that may be intrinsically linked through the concept of immunometabolism. Here, we combined bulk, single-cell, and spatial transcriptomics with cell-specific and spatially resolved metabolic analyses to systematically address the role of APOE across age, neuroinflammation, and AD pathology. RNAseq highlighted immunometabolic changes across the APOE4 glial transcriptome, specifically in subsets of metabolically distinct microglia enriched in the E4 brain during aging or following an inflammatory challenge. E4 microglia display increased Hif1a expression, a disrupted TCA cycle, and are inherently pro-glycolytic, while spatial transcriptomics and MALDI mass spectrometry imaging highlight an E4-specific response to amyloid that is characterized by widespread alterations in lipid metabolism. Taken together, our findings emphasize a central role for APOE in regulating microglial immunometabolism.
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Project description:RATIONALE
In spatial proteomics, matrix-assisted laser desorption/ionization (MALDI) imaging enables rapid and cost-effective peptide measurement. Yet, in situ peptide identification remains challenging. Therefore, this study aims to integrate the trapped ion mobility spectrometry (TIMS)-based parallel accumulation-serial fragmentation (PASEF) into MALDI imaging of peptides to enable multiplexed MS/MS imaging.
METHODS
An initial MALDI TIMS MS1 survey measurement is performed, followed by a manual generation of a precursor list containing mass over charge values and ion mobility windows. Inside the dual TIMS system, submitted precursors are trapped, separately eluted by their ion mobility and analyzed in a quadrupole time-of-flight device, thereby enabling multiplexed MALDI MS/MS imaging. Finally, precursors are identified by peptide to spectrum matching.
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This study presents the first multiplexed MALDI TIMS MS/MS imaging (iprm-PASEF) of tryptic peptides. Its applicability is showcased on two histomorphologically distinct tissue specimens in a 4-plex and 5-plex setup. Precursors were successfully identified by the search engine MASCOT in one single MALDI imaging experiment for each respective tissue. Peptide identifications were corroborated by liquid-chromatography tandem mass spectrometry experiments and fragment colocalization analyses.
CONCLUSIONS
In the present study, we demonstrate the feasibility of TIMS-based MALDI MS/MS imaging for the multiplexed and rapid identification of tryptic peptides in a spatial manner. Hence, it represents a first step towards the integration of MALDI imaging into the emerging field of spatial proteomics.
The datasets will be uploaded separately. This data set contains the PDX MS1 data. There are two tissues vissible on the.tif image. The relevant one is on the left side of the slide (away from the barcode).
2024-11-11 | MSV000096374 | MassIVE
Project description:RATIONALE
In spatial proteomics, matrix-assisted laser desorption/ionization (MALDI) imaging enables rapid and cost-effective peptide measurement. Yet, in situ peptide identification remains challenging. Therefore, this study aims to integrate the trapped ion mobility spectrometry (TIMS)-based parallel accumulation-serial fragmentation (PASEF) into MALDI imaging of peptides to enable multiplexed MS/MS imaging.
METHODS
An initial MALDI TIMS MS1 survey measurement is performed, followed by a manual generation of a precursor list containing mass over charge values and ion mobility windows. Inside the dual TIMS system, submitted precursors are trapped, separately eluted by their ion mobility and analyzed in a quadrupole time-of-flight device, thereby enabling multiplexed MALDI MS/MS imaging. Finally, precursors are identified by peptide to spectrum matching.
RESULTS
This study presents the first multiplexed MALDI TIMS MS/MS imaging (iprm-PASEF) of tryptic peptides. Its applicability is showcased on two histomorphologically distinct tissue specimens in a 4-plex and 5-plex setup. Precursors were successfully identified by the search engine MASCOT in one single MALDI imaging experiment for each respective tissue. Peptide identifications were corroborated by liquid-chromatography tandem mass spectrometry experiments and fragment colocalization analyses.
CONCLUSIONS
In the present study, we demonstrate the feasibility of TIMS-based MALDI MS/MS imaging for the multiplexed and rapid identification of tryptic peptides in a spatial manner. Hence, it represents a first step towards the integration of MALDI imaging into the emerging field of spatial proteomics.
All Datasets are uploaded separateley. This file contains the dataset for mouse kidney MS1 data.
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Project description:RATIONALE
In spatial proteomics, matrix-assisted laser desorption/ionization (MALDI) imaging enables rapid and cost-effective peptide measurement. Yet, in situ peptide identification remains challenging. Therefore, this study aims to integrate the trapped ion mobility spectrometry (TIMS)-based parallel accumulation-serial fragmentation (PASEF) into MALDI imaging of peptides to enable multiplexed MS/MS imaging.
METHODS
An initial MALDI TIMS MS1 survey measurement is performed, followed by a manual generation of a precursor list containing mass over charge values and ion mobility windows. Inside the dual TIMS system, submitted precursors are trapped, separately eluted by their ion mobility and analyzed in a quadrupole time-of-flight device, thereby enabling multiplexed MALDI MS/MS imaging. Finally, precursors are identified by peptide to spectrum matching.
RESULTS
This study presents the first multiplexed MALDI TIMS MS/MS imaging (iprm-PASEF) of tryptic peptides. Its applicability is showcased on two histomorphologically distinct tissue specimens in a 4-plex and 5-plex setup. Precursors were successfully identified by the search engine MASCOT in one single MALDI imaging experiment for each respective tissue. Peptide identifications were corroborated by liquid-chromatography tandem mass spectrometry experiments and fragment colocalization analyses.
CONCLUSIONS
In the present study, we demonstrate the feasibility of TIMS-based MALDI MS/MS imaging for the multiplexed and rapid identification of tryptic peptides in a spatial manner. Hence, it represents a first step towards the integration of MALDI imaging into the emerging field of spatial proteomics.
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Project description:RATIONALE
In spatial proteomics, matrix-assisted laser desorption/ionization (MALDI) imaging enables rapid and cost-effective peptide measurement. Yet, in situ peptide identification remains challenging. Therefore, this study aims to integrate the trapped ion mobility spectrometry (TIMS)-based parallel accumulation-serial fragmentation (PASEF) into MALDI imaging of peptides to enable multiplexed MS/MS imaging.
METHODS
An initial MALDI TIMS MS1 survey measurement is performed, followed by a manual generation of a precursor list containing mass over charge values and ion mobility windows. Inside the dual TIMS system, submitted precursors are trapped, separately eluted by their ion mobility and analyzed in a quadrupole time-of-flight device, thereby enabling multiplexed MALDI MS/MS imaging. Finally, precursors are identified by peptide to spectrum matching.
RESULTS
This study presents the first multiplexed MALDI TIMS MS/MS imaging (iprm-PASEF) of tryptic peptides. Its applicability is showcased on two histomorphologically distinct tissue specimens in a 4-plex and 5-plex setup. Precursors were successfully identified by the search engine MASCOT in one single MALDI imaging experiment for each respective tissue. Peptide identifications were corroborated by liquid-chromatography tandem mass spectrometry experiments and fragment colocalization analyses.
CONCLUSIONS
In the present study, we demonstrate the feasibility of TIMS-based MALDI MS/MS imaging for the multiplexed and rapid identification of tryptic peptides in a spatial manner. Hence, it represents a first step towards the integration of MALDI imaging into the emerging field of spatial proteomics.
The datasets will be uploaded separately. This data set contains the Kidney MSMS data. There is an additional Liver tissue vissible on the .tif image. This was used for another experiment
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