Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of PDH XL peptides in Bik1 at different conditions

ABSTRACT: Identification of PDH crosslinks in Bik1 at different conditions (phase separation and soluble)

INSTRUMENT(S): Q Exactive

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Federico Uliana

LAB HEAD: Federico Uliana

PROVIDER: PXD050930 | Pride | 2025-01-06

REPOSITORIES: pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	230322_QE1_ulianaf_YB_03_02.c.mzXML	Mzxml
	230322_QE1_ulianaf_YB_03_03.c.mzXML	Mzxml
	230322_QE1_ulianaf_YB_03_04.c.mzXML	Mzxml
	230322_QE1_ulianaf_YB_03_05.c.mzXML	Mzxml
	230322_QE1_ulianaf_YB_03_07.c.mzXML	Mzxml

Items per page:

1 - 5 of 122

Similar Datasets

Identification of XL peptides in Bik1 variants and different conditions

Project description:Identification of crosslinks in Bik1 variants and different conditions (phase separation, soluble, supernatant, pellet).

2025-01-06 | PXD050929 | Pride

Identification of Bik1 XL peptides (DSS)

Project description:Effect of different DSS concentrations and varying collision energy on the number of identified crosslinks.

2025-01-06 | PXD050928 | Pride

Targeted quantification of XL peptides in Bik1 variants and different conditions

Project description:Quantification of crosslinks in Bik1 variants and different conditions (phase separation, soluble, supernatant, pellet)

2025-01-06 | PXD055703 | Pride

To identify potential ubiquitin ligases that regulate BIK1 homeostasis

Project description:To identify potential ubiquitin ligases that regulate BIK1 homeostasis,A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. We using an optimized data analysis workflow,

2023-06-14 | GSE227628 | GEO

To identify potential ubiquitin ligases that regulate BIK1 homeostasis

Project description:To identify potential ubiquitin ligases that regulate BIK1 homeostasis

| PRJNA945931 | ENA

The Arabidopsis E3 ubiquitin ligase PUB4 regulates BIK1 and is targeted by a bacterial type-III effector

Project description:Plant immunity is tightly controlled by a complex and dynamic regulatory network, which ensures optimal activation upon detection of potential pathogens. Accordingly, each component of this network is a potential target for manipulation by pathogens. Here, we report that RipAC, a type III-secreted effector from the bacterial pathogen Ralstonia solanacearum, targets the plant E3 ubiquitin ligase PUB4 to inhibit pattern-triggered immunity (PTI). PUB4 plays a positive role in PTI by regulating the homeostasis of the central immune kinase BIK1. Before PAMP perception, PUB4 promotes the degradation of non-activated BIK1, while, after PAMP perception, PUB4 contributes to the accumulation of activated BIK1. RipAC leads to BIK1 degradation, which correlates with its PTI-inhibitory activity. RipAC causes a reduction in pathogen-associated molecular pattern (PAMP)-induced PUB4 accumulation and phosphorylation. Our results shed light on the role played by PUB4 in immune regulation, and illustrate an indirect targeting of the immune signalling hub BIK1 by a bacterial effector

2022-10-12 | PXD036739 | Pride

Data-independent acquisition protease-multiplexing enables increased proteome sequence coverage across multiple fragmentation modes

Project description:The use of multiple proteases has been shown to increase protein sequence coverage in proteomics experiments, but due to the additional sample preparation and analysis time required, it has not been widely adapted in routine proteomic workflows. While data-independent acquisition (DIA) has been primarily optimized for fragmenting tryptic peptides with beam type (bt)-CID, it has the potential to analyze multiplexed samples from different protease digests. Here we evaluate a DIA multiplexing method that combines three proteolytic digests (Trypsin, AspN, and GluC) into a single sample. We first optimize DIA conditions for both resonance excitation (re-CID) and bt-CID to determine the optimal consensus fragmentation conditions for tryptic and non-tryptic peptides, and apply these methods to a human cell line. We demonstrate that using this multiplexed approach results in similar protein identifications and quantitative performance as compared to trypsin alone, but enables up to a 63% increase in peptide detections, resulting in up to a 8% increase in average sequence coverage. Importantly, this resulted in 100% sequence coverage for numerous proteins, suggesting the utility of this approach in applications where sequence coverage is critical, such as proteoform analysis.

2022-03-18 | PXD027242 | Pride

RNxQuest: an extension to the xQuest pipeline enabling analysis of protein-RNA cross-linking/mass spectrometry data

Project description:The recently introduced cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) technique enables protein-RNA cross-links to be used as precisely localized distance restraints in de novo structural modelling. The novel data type requires a bespoke data analysis approach. The new RNxQuest Python package supports this approach. Here we demonstrate the performance of the new package using a mixture of novel and published datasets.

2023-09-06 | PXD039754 | Pride

Proteomics of Enriched Insulin Secretory Granules Fractionated by Size Exclusion Chromotography

Project description:Hybrid insulin peptides (HIPs) form in pancreatic beta-cells through the formation of peptide bonds between proinsulin fragments and other peptides. HIPs, which have been confidently identified in pancreatic islets by mass spectrometry, are targeted by CD4 T cells in subjects with Type 1 Diabetes (T1D), as well as by disease-triggering CD4 T cell clones in non-obese diabetic (NOD) mice. The mechanism(s) of HIP formation are currently poorly understood; however, it is well established that proteases can drive the formation of new peptide bonds in a side reaction during peptide bond hydrolysis. Here, we used a proteomic strategy on enriched insulin granules and identified cathepsin D (CatD) as the primary protease driving the specific formation of HIPs that are targeted by disease-relevant CD4 T cells in T1D. We also established that NOD islets deficient of cathepsin L (CatL), another protease that was implied in the formation of disease-relevant HIPs, contain elevated levels of HIPs, signifying a primary role for CatL in the proteolytic degradation of HIPs. In summary, our data suggest that CatD may be a therapeutic target in efforts to prevent or slow down the autoimmune destruction of beta-cells mediated by HIP-reactive CD4 T cells in T1D.

2023-11-16 | PXD032664 | Pride

Tissue Transglutaminase 2 has higher affinity for relaxed than for stretched fibronectin fibers

Project description:Chemical cross-linking coupled to mass spectrometry was used to study the interaction between fibronectin (Fn; full-length or gelatin-binding domain fragment = Fn 45) with tissue transglutaminase 2 in oxidized and non-oxidized form. The complexes were cross-linked with disuccinimidyl suberate (DSS) or a combination of pimelic dihydrazide (PDH) in combination with the zero-length cross-linking reagent, DMTMM.

2023-12-20 | PXD043976 | 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