GNPS - Rat brain MALDI Imaging negative ion mode
Ontology highlight
ABSTRACT:
INSTRUMENT(S): timsTOF fleX
ORGANISM(S): Sprague Dawley Rat
SUBMITTER: 
Robin Schmid
PROVIDER: MSV000092098 | GNPS | Mon Jun 05 01:30:00 BST 2023
REPOSITORIES: GNPS
Similar Datasets
Project description:Maldi imaging with NEDC matrix of a rat brain tissue section. Image was acquired with 50 um resolution. Ion mobility seperation enabled. Negative ion mode.
2023-06-05 | MSV000092098 | MassIVE
Project description:MALDI-imaging-guided Transcriptomics
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Project description:Rat brain tissues for imaging mass spectrometry were removed from animal organs, frozen on dry ice, and then stored at -80-degree C until analysis. 10-micrometer rat brain tissues were sectioned using a Leica CM 3050S Research Cryostat (Leica Biosystems, Wetzlar, Germany), prior to thaw mounting onto indium tin oxide-coated microscope slides (Delta Technologies, Loveland, CO, USA). 1,5-diaminonaphthalene (DAN) MALDI matrix layer was sublimated to the microscope slide using an in-house sublimation apparatus. MALDI imaging mass spectrometry was performed on a 7T solariX Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer equipped with a dynamically harmonized ParaCell XR (Bruker Daltonics, Bremen, Germany). Analysis was performed in negative ion mode from m/z 400 to 2000 with ~0.5 s time-domain transient length, resulting in a resolution of ~35,000 FWHM at m/z ~760. The MALDI source is equipped with a Smartbeam II Nd:YAG MALDI laser and was used to sample at a pixel spacing of 100 micrometers in the x and y dimensions using 200 laser shots per pixel (large laser focus, 2 kHz frequency) with Smart Walk enabled.
2024-06-23 | MSV000095124 | MassIVE
Project description:Autosomal recessive polycystic kidney disease is a severe, monogenetically inherited kidney and liver disease and PCK rats carrying the orthologous mutant gene serve as a model of human disease. We combined selective MALDI imaging of sulfated kidney lipids and Fisher discriminant analysis of imaging data sets for identification of candidate lipid markers of progressive disease in PCK rats. Our study highlights strong increases in lower mass lipids as main classifiers of cystic disease. Structure determination by high resolution mass spectrometry identifies these altered lipids as taurine-conjugated bile acids. Beside increased levels of serum-cholesterol these sulfated lipids are selectively elevated in the PCK rat model but not in models of related hepatorenal fibrocystic diseases suggesting that they be molecular markers of the disease. Genome-scale gene expression profiling of PCK and SD livers as control was performed to attempt elucidation of some of the underlying mechanisms leading to increases of cholesterol and taurine-conjugated bile acids in the PCK rat. Several pathways were found to be changed in cystic livers with up regulation or down regulation of important gene sets. Enhanced expression of steroid biosynthesis genes might result in the observed increased levels of cholesterol. In contrast, primary bile acid biosynthesis was found to be down regulated in diseased livers. These findings might be explained by compensatory mechanisms of liver metabolism to reduce toxic levels of accumulated bile acids. Snap-frozen liver tissue of 10 week old rats were subjected for RNA extraction and hybridization on Affymetrix microarrays to perform genome-scale gene expression profiling of n = 6 diseased PCK and n = 6 Sprague Dawley rat livers as control.
2013-12-01 | E-GEOD-48357 | biostudies-arrayexpress
Project description:We developed and validated ‘HIT-MAP’ (High-resolution Informatics Toolbox in MALDI-MSI Proteomics), an open-source bioinformatics workflow using peptide mass fingerprint analysis and a dual scoring system to computationally assign peptide and protein annotations to high mass resolution MSI datasets, and generate customisable spatial distribution maps. The uploaded files are an example dataset for the HiTMaP proteomics search engine, designed for MALDI-imaging proteomics annotation. The example data files contain one bovine lens tissue section and one mouse brain tissue section. The ID folder contains the protein/peptide identification result for each tissue segment, and the summary folder contains the protein cluster images.
2021-05-17 | PXD025486 | Pride
Project description:Rat brain tissues for imaging mass spectrometry were removed from animal organs, frozen on dry ice, and then stored at -80-degree C until analysis. 10-micrometer rat brain tissues were sectioned using a Leica CM 3050S Research Cryostat (Leica Biosystems, Wetzlar, Germany), prior to thaw mounting onto indium tin oxide-coated microscope slides (Delta Technologies, Loveland, CO, USA). 1,5-diaminonaphthalene (DAN) MALDI matrix layer was sublimated to the microscope slide using an in-house sublimation apparatus. MALDI imaging mass spectrometry was performed on a 7T solariX Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer equipped with a dynamically harmonized ParaCell XR (Bruker Daltonics, Bremen, Germany). Analysis was performed in negative ion mode from m/z 400 to 2000 with ~0.5 s time-domain transient length, resulting in a resolution of ~35,000 FWHM at m/z ~760. The MALDI source is equipped with a Smartbeam II Nd:YAG MALDI laser and was used to sample at a pixel spacing of 100 micrometers in the x and y dimensions using 200 laser shots per pixel (large laser focus, 2 kHz frequency) with Smart Walk enabled.
2024-06-23 | MSV000095124 | GNPS
Project description:Autosomal recessive polycystic kidney disease is a severe, monogenetically inherited kidney and liver disease and PCK rats carrying the orthologous mutant gene serve as a model of human disease. We combined selective MALDI imaging of sulfated kidney lipids and Fisher discriminant analysis of imaging data sets for identification of candidate lipid markers of progressive disease in PCK rats. Our study highlights strong increases in lower mass lipids as main classifiers of cystic disease. Structure determination by high resolution mass spectrometry identifies these altered lipids as taurine-conjugated bile acids. Beside increased levels of serum-cholesterol these sulfated lipids are selectively elevated in the PCK rat model but not in models of related hepatorenal fibrocystic diseases suggesting that they be molecular markers of the disease. Genome-scale gene expression profiling of PCK and SD livers as control was performed to attempt elucidation of some of the underlying mechanisms leading to increases of cholesterol and taurine-conjugated bile acids in the PCK rat. Several pathways were found to be changed in cystic livers with up regulation or down regulation of important gene sets. Enhanced expression of steroid biosynthesis genes might result in the observed increased levels of cholesterol. In contrast, primary bile acid biosynthesis was found to be down regulated in diseased livers. These findings might be explained by compensatory mechanisms of liver metabolism to reduce toxic levels of accumulated bile acids.
2013-12-01 | GSE48357 | GEO
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.
On the same slice a mouse liver was measured for a different experiment.
2024-11-11 | MSV000096373 | 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.
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.
The datasets will be uploaded separately. This data set contains the PDX MSMS 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 | MSV000096376 | MassIVE