Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Elucidating the underlying mechanism behind AtMC1C220A autoimmune phenotype through the study of AtMC1C220A interactors at the microsomal and total fractions.

ABSTRACT: Identification of Metacaspase 1 (AtMC1) interacting partners using IP-MS

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

SUBMITTER: Farnusch Kaschani

LAB HEAD: Farnusch Kaschani

PROVIDER: PXD049206 | Pride | 2025-03-04

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ACE_0662_JS01.raw	Raw
	ACE_0662_JS02.raw	Raw
	ACE_0662_JS03.raw	Raw
	ACE_0662_JS04.raw	Raw
	ACE_0662_JS05.raw	Raw

Items per page:

1 - 5 of 33

Similar Datasets

Effect of Bion (BTH treatment) in GST activities on 6-week old A.thaliana plants

Project description:The goal of this project was to investigate GSTs labelled by GST-G probe in non-treated Arabidopsis (Water samples: Click control vs GST-G) or GSTs activated upon Bion treatment of Arabidopsis (Water GST-G vs Bion GST-G).

2024-01-26 | PXD045884 | Pride

In vitro phosphorylation of Dam1 complex and Bim1 by Mps1

Project description:The Dam1 complex (Dam1c) of Saccharomyces cerevisiae is a major microtubule binding component of the yeast kinetochore. Phosphorylation of various kinetochore proteins by mitotic kinases such as Mps1 are known to modulate the function of these proteins and regulate protein-protein interaction. The Dam1 subunit of Dam1c was previously demonstrated to be phosphorylate by Mps1 (residues S13, S49, S217, S218, S221, S232. In this project we mapped additional phosphor sites on components of the Dam1 complex by mass spectrometry after in vitro phosphorylation as a first step to understand the physiological function of these phosphorylation events.

2024-05-22 | PXD047005 | Pride

Confirmation of replication interactome of TopBP1 using proximity-dependent biotinylation MS

Project description:Goal of the Experiment is to confirm the replication interactome of TopBP1 using stabile 293 FlpIn cell lines expressing TopBP1 adapter fused to APEX2. Proteins in its close proximity will become biotinylated by APEX2, thereby enabling the pulldown of biotinylated proteins and thus, replication involved substrates of TopBP1

2024-05-21 | PXD040000 | Pride

Using Proteomics for an Insight into the Performance of Activated Sludge

Project description:The performance of a lab-scale wastewater treatment plant during the start-up phase was investigated. A period of varying pH resulted in the loss of ammonium removal efficiency together with a decrease in the specific autotrophic oxygen uptake rate (OUR). From the OUR, it was inferred that the ammonium oxidizing bacteria (AOB) were inhibited by the fluctuation in the pH values. However, OUR alone could not provide the information as to how the AOB were affected at the molecular level. To gain a better insight, shotgun proteomic method was used in this work to quantify the total proteins in the system. Label-free quantification (LFQ) showed that during the time of poor ammonium removal, the marker enzyme hydroxylamine oxidase found in Nitrosomonas sp. was at the lowest LFQ intensity. Based on these results, proteomics has the potential to be used as a monitoring tool. Nevertheless, there are still some restrictions when measuring activated sludge using proteomic method such as the availability of a suitable proteomic database. In this paper, we describe our experience of using publicly available database for identification of activated sludge proteins.

2020-05-18 | PXD014156 | Pride

Ubiquitin-independent disassembly by a p97 AAA-ATPase complex drives PP1 holoenzyme formation

Project description:Protein phosphatase-1 (PP1) dephosphorylates a broad spectrum of substrates to regulate a myriad of cellular processes. This functional diversity relies on the ordered assembly of alternative PP1 holoenzymes. Here, we show that newly synthesized PP1 is first held in an inactive complex by its partners SDS22 and inhibitor-3 (I3) that needs to be disassembled by the p97 AAA-ATPase to promote exchange to substrate specifiers. Unlike p97-mediated degradative processes that require the Ufd1-Npl4 ubiquitin adapters, p97 is targeted to PP1 by p37 and related adapter proteins. Reconstitution with purified components revealed direct interaction of the p37 SEP domain with I3 without the need of ubiquitination, and ATP-driven pulling of I3 into the central channel of the p97 hexamer, which triggers dissociation of I3 and SDS22. Thus, we establish regulatory ubiquitin-independent protein complex disassembly as part of the functional arsenal of p97 and define an unanticipated essential step in PP1 biogenesis that illustrates the molecular challenges of ordered subunit exchange.

2018-10-23 | PXD010750 | Pride

Effect of Cpd1 on melanoma proteome

Project description:Investigation of the time dependent effect of Cpd1 (small molecule interactor) on the proteome composition of melanoma WM3734 line by label-free quantification using mass spectrometry. The goal was to identify which protein abundances are increased upon treatment with Cpd1. Melanoma cell line WM3734 was treated with Cpd1 and with the control DMSO. Samples were taken at two time points, 24h and 72h.

2022-03-14 | PXD008757 | Pride

Isolation and characterisation of a 14kDa adhesin protein from Rhizobium leguminosarum biovar viciae 3841

Project description:In this project we aimed to identify a 14 kDa adhesin protein from Rhizobium leguminosarum biovar viciae 3841 unsing in gel digestion coupled to LC-MS/MS.

2024-08-19 | PXD029089 | Pride

Proteomic differences in the synovial fluid of patients undergoing septic or aseptic revision arthroplasty

Project description:In 21 patients undergoing revision arthroplasty due to septic or aseptic implant loosening, synovial fluid was collected intraoperatively after opening the joint capsule. In a proteomic MS approach, we wanted now to investigate these synovial fluids for novel proteogenic markers of periprosthetic infections.

2024-05-21 | PXD047507 | Pride

ct of PROTAC #89, which targets an endogenously SNAP-tagged clathrin light chain, on the HAP1 cell proteome

Project description:We would like to investigate what effect degradation of the clathrin light chain has on the HAP1 proteome. We therefore tagged the clathrin light chain (CLC) in HAP1 cells endogenously with a SNAP-tag via CRISPaint. The degradation of the SNAP-tagged protein is induced by the addition of a SNAP-PROTAC (PROTAC #89). The proteomes of a short (6 h) and long (24 h) treatment with PROTAC #89 are compared against the corresponding DMSO controls using LFQ.

2025-05-06 | PXD049283 | Pride

Activity profiling of αlpha-glycosidases in plants

Project description:With nearly 140 α-glycosidases in 14 different families, plants are well equipped with enzymes that can break the α-glucosidic bonds in a large diversity of molecules. Here, we introduce activity profiling of α-glycosidases in plants using α-configured cyclophellitol aziridine probes carrying various fluorophores or biotin. In Arabidopsis, these probes label members of the GH31 family of Glycosyl Hydrolases, including ER-resident α-glucosidase-II RSW3/PSL5 and Golgi-resident α-mannosidase-II HGL1, which both trim N-glycans on glycoproteins. We also detect the active state of extracellular α-glycosidases such as α-xylosidase XYL1, which acts on xyloglucan in the cell wall to promote cell expansion, and α-glucosidase AGLU1, which acts in starch hydrolysis and can suppress fungal invasion. α-glycosidase labelling causes specific signals at 100-130 kDa that are pH-dependent and can be supressed by α-glycosidase inhibitors miglitol and acarbose. The α-glycosidase probes display similar miglitol-sensitive signals in leaf extracts of in a broad range of plant species. To show its use on a non-model plant, we applied glycosidase activity profiling on Crocus sativa, a cash crop for the production of saffron spice. Using a combination of biotinylated glycosidase probes, we identified and quantified 70 active glycosidases in stigma stages 1 and 4 of saffron (Crocus sativa L.), ten of which are differentially active. We also uncover massive changes in hydrolase activities in corms upon infection with Fusarium oxysporum using multiplex fluorescent labelling in combination with probes for serine hydrolases and cysteine proteases. These experiments demonstrate the ease by which active α-glycosidases and other hydrolases can be displayed in non-model plants.

2018-05-17 | PXD009014 | 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