Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The Proteomics landscape of aortic aneurysm

ABSTRACT: The Proteomics landscape of aortic degeneration and aortopathy

INSTRUMENT(S): timsTOF Pro

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Aorta

SUBMITTER: Zhang Weijia

LAB HEAD: Weijia Zhang

PROVIDER: PXD043052 | Pride | 2024-12-10

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Aortic_fraction_1.zip	Other
	Aortic_fraction_2.zip	Other
	Aortic_fraction_3.zip	Other
	Aortic_fraction_4.zip	Other
	Aortic_fraction_5.zip	Other

Items per page:

1 - 5 of 162

Similar Datasets

The Proteomics landscape of human aorta and mice aorta

Project description:NOTCH1 mutation and deficiency is etiologically associated to aortopathy combined with bicuspid aortic valve malformation; currently no medication is available for its treatment. Therefore, in this study, our focus turns to seeking the key downstream target genes and pharmacotherapeutic possibilities for NOTCH1 deficient aortopathy.

2024-12-10 | PXD044019 | Pride

Comparative DDA and DIA-PASEF proteomics profiling of cross-kingdom macrophage infection reveals new mechanisms driving pathogen virulence

Project description:Opportunistic infections of the respiratory tract often succeed under a weakened immune response caused by an underlying illness or hospitalization. The human fungal pathogen, Cryptococcus neoformans, and the bacterial pathogen, Klebsiella pneumoniae, are both well-characterized microbes that cause severe infections within immunocompromised individuals. In this study, we simulate a concentration-dependent pulmonary coinfection of a bacterial and fungal pathogen, and profile the proteomic changes by DDA vs. DIA. Dual perspective profiling provides new insights into host defense regulation of infection and pathogenic mechanisms of invasion.

2024-08-13 | PXD054527 | Pride

Synchro-PASEF slices peptide precursors enabling specific fragment extraction and interference removal in data independent acquisition

Project description:Data independent acquisition methods have become increasingly popular in mass spectrometry (MS)-based proteomics because they enable parallel and continuous acquisition of fragment spectra. However, these advantages come with the challenge of correctly reconstructing the precursor-fragment relationship in these highly multiplexed spectra for reliable identification and quantification. Here we introduce a scan mode for the combination of trapped ion mobility spectrometry (TIMS) with parallel accumulation – serial fragmentation (PASEF) that naturally and continuously follows the ion cloud in ion mobility and peptide mass dimensions as opposed to the step functions we employed before. Termed synchro-PASEF, it increases fragment yield several fold at sub-second cycle times. The quadrupole selection window moves synchronously through the mass and ion mobility range, deconvoluting the DIA spectra and defining precursor-quadrupole relationships. In this process, the quadrupole slices through the peptide precursors, which separates fragment ion signals of each precursor into adjacent synchro-PASEF scans. This precisely defines precursor – fragment relationship in ion mobility and mass dimensions. Importantly, the two parts of the fragment ion transitions in synchro-PASEF provide a further dimension of specificity via a lock and key mechanism. This is especially advantageous for quantification, where signals from interfering precursors in the dia selection window only affect the top or bottom part of the fragment ion, allowing them to be filtered out. In this paper, we establish the defining features of synchro-PASEF and explore its potential for proteomics analyses.

2023-03-10 | PXD037766 | Pride

A framework for ultra-low input spatial tissue proteomics

Project description:Spatial tissue proteomics combining microscopy-based cell phenotyping with ultrasensitive mass spectrometry (MS)-based proteomics is an emerging and powerful concept for the study of cell function and heterogeneity in health and disease. However, optimized workflows that preserve morphological information for image-based phenotype discovery and maximize proteome coverage of few or even single cells from laser microdissected archival tissue, are currently lacking. Here, we report a robust and scalable workflow for the proteomic analysis of ultra-low input formalin-fixed, paraffin-embedded (FFPE) material. Benchmarking in the murine liver resulted in up to 2,000 quantified proteins from single hepatocyte contours and nearly 5,000 proteins from 50-cell regions with high quantitative reproducibility. Applied to human tonsil, we profiled 146 microregions including spatially defined T and B lymphocyte niches and quantified cell-type specific markers, cytokines, immune cell regulators and transcription factors. These rich data also highlighted proteome dynamics in spatially defined zones of activated germinal centers, illuminating sites undergoing active B-cell proliferation and somatic hypermutation. Our results demonstrate the power of spatially-resolved proteomics for tissue phenotyping by integrating high-content imaging, laser microdissection, and ultrasensitive mass spectrometry. This approach has broad implications for a wide range of biomedical applications, including early disease profiling, drug target discovery and biomarker research.

2023-11-08 | PXD042367 | Pride

Proteomic characterization of 1,000 human and murine neutrophils freshly isolated from blood and sites of sterile inflammation

Project description:Neutrophils, crucial player in inflammation, present a significant challenge in comprehensive molecular characterization due to limited availability (~1,000 cells) in inflamed sites like steady state infiltration. Prior proteomic studies typically required millions of neutrophils, posing difficulties when dealing with limited samples. This study introduces a ‘low-cell proteome’ workflow for neutrophils, integrating S-trap micro column-based digestion with DIA PASEF to investigate their functional dynamics within individual inflamed site.This method enable protein profiling of 1,000 isoated resting circulatory neutrophils with broad dynamic range in a reproducible manner.Furthermore, we applied this integrated approach to investigate the change in neutrophil proteome under different physiological and pathological conditions, including brain infiltration following stroke in mice and transmigration to the oral cavity post-treatment with tabasco in humans. Our comprehensive proteomic analysis provides insights into the distinct behavioral responses of neutrophils in these inflammatory contexts compared to their circulating counterparts.

2024-10-11 | PXD050682 | Pride

dia-PASEF analysis of human amygdala in Parkinson’s disease

Project description:dia-PASEF analysis of human amygdala in Parkinson’s disease

2024-01-26 | PXD043503 | Pride

dia-PASEF analysis of human amygdala in Alzheimer’s disease

Project description:dia-PASEF analysis of human amygdala in Alzheimer’s disease

2023-06-28 | PXD038322 | Pride

Data-Independent Acquisition Represents a Promising Alternative for Fast Photochemical Oxidation of Proteins (FPOP) Samples Analysis

Project description:We propose a novel approach for FPOP data analysis, utilizing DIA data. The HbHp protein complex was analyzed by FPOP and measured on timsToF SCP in DIA, DDA and MS modes. The IDs of modified peptides were quantified for each acquisition mode and the extent of modification was calculated on the level of peptides. The reproducibility was evaluated by coefficients of variation.This work was mainly financially supported by the Czech Science Foundation (22-27695S), the Technology Agency of the Czech Republic (ODEEP-EU TH86010001), the Ministry of Education, Youth and Sports of the Czech Republic grant PHOTOMACHINES - Photosynthetic cell redesign for high yields of therapeutic peptides (CZ.02.01.01/00/22_008/0004624) and the Academy of Sciences of the Czech Republic (RVO: 61388971).

2024-07-08 | PXD050132 | Pride

DDA-PASEF and diaPASEF acquired A549/K562 proteomic datasets with deliberate batch effects

Project description:We generated two comprehensive large-scale proteomics datasets with deliberate batch effects using the latest parallel accumulation-serial fragmentation in both Data-Dependent and Data-Indepentdent Acquisition modes. This dataset contain a balanced two-class design (cell lines: A549 vs K562), allowing for investigating mixed effects from class, batch and acquisition method. Investigators can also compare and integrate DDA and DIA platforms, delve into the various patterns and mechanisms of missing values, benchmark batch effects correction algorithms and assess confounding between different technical issues.

2023-11-21 | PXD041421 | Pride

DDA-PASEF and diaPASEF acquired HCC1806/HS578T proteomic datasets with deliberate batch effects

Project description:We generated two comprehensive large-scale proteomics datasets with deliberate batch effects using the latest parallel accumulation-serial fragmentation in both Data-Dependent and Data-Indepentdent Acquisition modes. This dataset contain a balanced two-class design (cell lines: HCC1806 vs HS578T), allowing for investigating mixed effects from class, batch and acquisition method. Investigators can also compare and integrate DDA and DIA platforms, delve into the various patterns and mechanisms of missing values, benchmark batch effects correction algorithms and assess confounding between different technical issues.

2023-11-21 | PXD041391 | Pride