Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

In vivo stress reporters as early biomarkers of the cellular changes associated with progeria

ABSTRACT: Study of progeria reporter mouse model using histology, proteomics and western-blotting.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Mus Musculus (mouse)

SUBMITTER: Florian Weiland

LAB HEAD: Francisco Inesta-Vaquera

PROVIDER: PXD033518 | Pride | 2023-03-11

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20210103_Mus_musculus_CanonicalIsoforms.fasta	Fasta
	20210104_Total_Proteome_MQ_parameters.xml	Xml
	Francisco_total_proteome_f1.raw	Raw
	Francisco_total_proteome_f10.raw	Raw
	Francisco_total_proteome_f11.raw	Raw

Items per page:

1 - 5 of 19

Publications

In vivo stress reporters as early biomarkers of the cellular changes associated with progeria.

Inesta-Vaquera Francisco F Weiland Florian F Henderson Colin J CJ Wolf Charles Roland CR

Journal of cellular and molecular medicine 20221006 21

Age-related diseases account for a high proportion of the total global burden of disease. Despite recent advances in understanding their molecular basis, there is a lack of suitable early biomarkers to test selected compounds and accelerate their translation to clinical trials. We have investigated the utility of in vivo stress reporter systems as surrogate early biomarkers of the degenerative disease progression. We hypothesized that cellular stress observed in models of human degenerative dise ...[more]

PMID: 36201626

Similar Datasets

CDKL5 - nuclear substrates - Validation

Project description:Validation dataset for the kinase substrates identified in the phosphoproteomics dataset.

2020-12-10 | PXD022975 | Pride

Identification of proteins interacting with the NEK1-C21ORF2 complex

Project description:We and others have found that the NEK1 kinase interacts with the C21ORF2 protein. Gel filtration indicated there may be other proteins in the complex. We tried to identify such proteins by immunoprecipitating endogenous NEK1 from cells and subjecting the precipitates to mass spectrometry. We also immunoprecipitated endogenous NEK1 from cells and subjected the precipitates to mass spectrometry. To find the full complement of NEK1 interactors, NEK1 was immunoprecipitated from ARPE-19 parental cells, and NEK1-KO cells were to control for non-specific binding. Five biological replicates were used per cell line, and after trypsinization of the precipitates, peptides were labelled with tandem mass tags (TMT) enabling quantitative mass spectrometric analysis of the 10 samples which were pooled and analysed in parallel. To find the full complement of C21ORF2 interactors, C21ORF2 was immunoprecipitated from ARPE-19 parental cells, and C21ORF2-KO cells were to control for non-specific binding. Five biological replicates were used per cell line, and after trypsinization of the precipitates, peptides were labelled with tandem mass tags (TMT) enabling quantitative mass spectrometric analysis of the 10 samples which were pooled and analysed in parallel.

2023-05-09 | PXD036410 | Pride

Facilitating in situ cross-linking and mass spectrometry by antibody-based protein enrichment

Project description:Cross-linking of living cells followed by mass spectrometry identification of cross-linked peptides (in situ CLMS) is an emerging technology to study protein structures in their native environment. One of the inherent difficulties of this approach is the high complexity of the samples following cell lysis. This difficulty largely limits the identification of cross-links to the more abundant proteins in the cell. Here, we describe a targeted approach in which an antibody pulls a specific protein-of-interest out of the lysate. Mass spectrometry analysis of the protein material that binds to the antibody can then identify considerably more cross-links on the antibody target and its interactors. By using an antibody against the CCT chaperonin, we obtained over two hundred cross-links that provide in situ evidence for the subunit arrangement of CCT and its main interactions with prefoldin. Antibodies against tubulin likewise provided in situ evidence for the structure of the microtubule including the seam. Finally, the approach was also successful in identifying cross-links on a protein expressing at very low amounts (tau in non-neuronal cells). These results demonstrate the general applicability of antibody-based sample simplification for in situ CLMS.

2022-06-09 | PXD025099 | Pride

Mass spectrometry study of formaldehyde cross-linking of structured proteins

Project description:Formaldehyde is a widely used fixative in biology and medicine. The current chemical model for formaldehyde cross-linking of proteins is the formation of a methylene bridge that incorporates one carbon atom into the link. Here, we present mass spectrometry data that largely refute this model. Instead, our data show that cross-linking of structured proteins mainly involves a reaction that incorporates two carbon atoms into the link. Under MS/MS fragmentation, the link cleaves symmetrically to yield unusual fragments with a modification of one carbon atom. We apply this new understanding of the underlying cross-linking chemistry to the structural approach of cross-linking coupled to mass spectrometry. First, we cross-linked a mixture of purified proteins with formaldehyde. Our new analysis readily identified tens of cross-links from these proteins, which fit well with their atomic structures. We then perform in-situ cross-linking of human cells in culture. We identified 469 intra-protein and 90 inter-protein cross-links, which also fit well with available atomic structures. Interestingly, many of these cross-links could not be mapped onto a known structure and thus provide new structural insights. We highlight an example in which formaldehyde cross-links localize the binding site of βNAC on the ribosome. We also find several interactions of actin with auxiliary proteins. Our findings not only expand our understanding of formaldehyde reactivity and toxicity, but also clearly demonstrate how to use this potent reagent for structural studies.

2020-06-25 | PXD015435 | Pride

The structural heterogeneity of α-synuclein is governed by several distinct subpopulations with interconversion times slower than milliseconds

Project description:The intrinsically disordered protein, α-synuclein, implicated in synaptic vesicle homeostasis and neurotransmitter release, is also associated with several neurodegenerative diseases. The different roles of α-synuclein are characterized by distinct structural states (membrane-bound, dimer, tetramer, oligomer, and fibril), which are originated from its various monomeric conformations. The pathological states, determined by the ensemble of α-synuclein monomer conformations and dynamic pathways of interconversion between dominant states, remain elusive due to their transient nature. Here, we use inter-dye distance distributions from bulk time-resolved Förster resonance energy transfer as restraints in discrete molecular dynamics simulations to map the conformational space of the α-synuclein monomer. We further confirm the generated conformational ensemble in orthogonal experiments utilizing far-UV circular dichroism and cross-linking mass spectrometry. Single-molecule protein-induced fluorescence enhancement measurements show that within this conformational ensemble, some of the conformations of αsynuclein are surprisingly stable, exhibiting conformational transitions slower than milliseconds. Our comprehensive analysis of the conformational ensemble reveals essential structural properties and potential conformations that promote its various functions in membrane interaction or oligomer and fibril formation.

2022-10-14 | PXD024671 | Pride

FACS sorted podocytes, mesangial cells

Project description:FACS sorted glomerular kidney cells from a single mouse were subjected to proteomics.

2022-10-13 | PXD016237 | Pride

Analysis of mouse glomerular cells

Project description:Protoemics of endothelia, podocytes, mesangial cells from mouse

2022-06-09 | PXD016238 | Pride

Deep mapping of the mouse podocyte proteome

Project description:We analyzed the proteome of mouse FACS-sorted podocytes. We compared podocytes ("green cells") with non-podocyte ("red cells") cells of the glomerulus.

2018-06-21 | PXD003306 | Pride

Analysis of the effect of CHX on the cultured podocyte proteome

Project description:We analyzed the effect of Cycloheximide (CHX) on the podocyte proteome in both the differentiated and undifferentiated state.

2018-05-01 | PXD006886 | Pride

Analysis of the cilia membrane proteome by cmAPEX

Project description:APEX was targeted to the primary cilium of mouse IMCD cells using a 5HT6-APEX-GFP fusion construct. Proximity labling was performed using incubation with biotinphenol and H2O2. For details, please see the methods section of the accompanying paper.

2017-07-18 | PXD005201 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data