Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

4D-FastDIA quantitative phosphorylation modification omics analysis before and after expression of Salmonella effector SteC in RAW264.7 cell

ABSTRACT: The Salmonella effector SteC is the only protein kinase encoded by Salmonella pathogenicity island 2 that is secreted through the type III secretion system. SteC is known to trigger actin rearrangement via the phosphorylated MEK pathway, and our previous experiments demonstrated that the migration process of macrophages found during Salmonella infection is dependent on the rearrangement of the host cell actin backbone and the action of SteC.To further investigate the target of SteC in the host, we constructed a SteC-RAW264.7 cell line and performed phosphomics analysis using 4D-FastDIA to identify the direct substrates of SteC that trigger macrophage migration and lead to cytoskeletal rearrangement.

INSTRUMENT(S): timsTOF

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Cell Culture

SUBMITTER: Min Zhang

LAB HEAD: Min Zhang

PROVIDER: PXD042038 | Pride | 2024-02-22

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

Comparative Phenotypic, Proteomic, and Phosphoproteomic Analysis Reveals Different Roles of Serine/Threonine Phosphatase and Kinase in the Growth, Cell Division, and Pathogenicity of Streptococcus suis

Project description:To investigate the influence of STP and STK on protein expression in S. suis, we performed a comparative proteomics analysis with the WT, Δstp, and Δstk strains using liquid chromatography mass spectrometry/mass spectrometry (LC-MS/MS).STK and STP are serine/threonine kinases and phosphatases, respectively. Therefore, we next analyzed the changes in the abundance of serine/threonine phosphorylated proteins in Δstp and Δstk compared with the WT strain.

2021-11-30 | PXD029994 | Pride

Tomato fruit ripening Phosphoproteome

Project description:Through the quantitative proteomics research strategy of TMT labeling and phosphorylation enrichment technology and high-resolution liquid chromatography-mass spectrometry, this project carried out the quantitative research of phosphorylated proteomics. In this study, a total of 6227 phosphorylation sites were identified, of which 4501 sites contained quantitative information. In order to ensure the high reliability of the results, we used the standard of localization probability>0.75 to filter the identification data, and finally determined 4842 phosphorylation sites located on 2328 proteins, of which 4,011 sites of 1996 proteins contained quantitative Information, and use the filtered data for subsequent bioinformatics analysis. If 1.5 times is the change threshold, t-test p-value<0.05 is the standard, and after full proteomics normalization, then among the quantified phosphorylation sites, there are 161 in the AC-B4vsAC-MG comparison group The modification level of the locus was up-regulated, and the modification level of 364 sites was down-regulated (for more information about the differences between the comparison groups, please see the main body of the report). Based on the above data, we conducted a systematic bioinformatics analysis of proteins containing quantitative information, including protein annotation, functional classification, functional enrichment, and cluster analysis based on functional enrichment. And combining the above information provides a reference direction for the downstream in-depth research based on proteomics.

2022-02-17 | PXD027844 | Pride

Global Phosphoproteomics Reveals Molecular Networks in Systemic Lupus Erythematosus

Project description:Systemic lupus erythematosus (SLE) is a systemic and heterogeneous autoimmune disease for which its treatment and phosphorylation-dependent regulatory mechanism remain elusive. Here, we aim to explore the molecular mechanism of phosphorylation regulation for SLE. We employed high-throughput Phosphoproteomics of peripheral blood mononuclear cells (PBMCs) from 126 patients with SLE remission stage (SLE_S), 70 patients with SLE active stage (SLE_A), 160 patients with RA, and 135 healthy controls (HC). An independent cohort that included 60 SLE_S, 35 SLE_A, 50 RA and 40 HC was used to validate the phosphosites via parallel reaction monitoring (PRM). We revealed upregulated pathways involved in cell adhesion and migration in patients with SLE (SLE_S and SLE_A) compared with HCs and RA. Expression pattern clustering analysis revealed several specifically upregulated phosphosites, and the leukocyte transendothelial migration was specifically enriched in SLE_A. We predicted several key kinases including MAP3Ks, MAP2Ks, IKKB and TBK1, and found that upregulated kinase activity is associated with increased phosphorylation of VCL, TLN1 and VAPB by kinases-substrate network analysis. These phosphorylated proteins also regulate the pathways related to cell adhesion and migration, and which have not been implicated in previous studies of SLE. Moreover, we validated these phosphosites with the same trend as 4D-LFQ data, including LCP1 S5, TLN1 S1201, TLN1 S1225, VCL S275 and VCL S579. In summary, the present study elucidates the changes of phosphosites, kinases and pathways in SLE, and may provide potentially novel targets for further mechanism exploration.

2023-03-11 | PXD025399 | Pride

Global Phosphoproteomics Reveals Molecular Networks in Systemic Lupus Erythematosus

2023-03-11 | PXD025076 | Pride

Global Phosphoproteomics Reveals Molecular Networks in Systemic Lupus Erythematosus

2023-03-11 | PXD025559 | Pride

A Global Phosphorylation Atlas of Proteins within Pathological Site of Rotator Cuff Tendinopathy

Project description:Phosphorylation, as one of the most important and well-studied post-translational modifications, is tightly associated with protein activity and protein functional regulation. Here in this study, we generated a global protein phosphorylation atlas within the pathological site of human RCT patients by using Tandem Mass Tag (TMT) labeling combining with mass spectrometry. GO enrichment analyses and KEGG pathway analyses were performed. At last, a weighted kinase-site phosphorylation network was built to identify potentially core kinase.

2021-12-24 | PXD029866 | Pride

Phosphoproteome of SHVV-infection CCO cell

Project description:SHVV-infected CCO cells at 24 h post infection and mock CCO cells were used for 4D label-free phosphoproteome sequencing to identify phosphorylated sites on proteins of SHV.

2024-01-26 | PXD041500 | Pride

Explore the lactation function of Protein phosphorylation sites in goat mammary tissues by phosphoproteome

Project description:Background: Protein phosphorylation plays an important role in lactation. Differentially modified phosphorylation sites between peak lactation (PL, 90 days postpartum) and late lactation (LL, 280 days postpartum) were investigated using an integrated approach, namely, liquid chromatography with tandem mass spectrometry (LC-MS/MS) and tandem mass tag (TMT) labelling, to know the molecular changes in different stages of goat mammary tissues. Results: A total of 1,938 (1,111 up-regulated, 827 down-regulated) differentially modified phosphorylation sites of 1,172 proteins were identified (P values < 0.05 and fold change of phosphorylation ratios > 1.5). In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that calcium signalling pathway, oxytocin signalling pathway and MAPK signalling pathway were enriched. The results of western blot showed phosphorylation levels of ACACA, EIF4EBP1 and IRS1 increased and JUN decreased in PL compared with LL. The results were consistent with the results of phosphoproteome. Conclusions: In this study, we first differentially proteins modified phosphorylation sites between PL and LL in goat mammary tissues. On the other hand, these results analysis indicate that multiple differentially modified phosphorylation sites of FASN, ACACA, mTOR, PRKAA, IRS1, RPS6KB, EIF4EBP1, TSC2 and proteins of Calcium signalling pathway, Oxytocin signalling pathway, and MAPK signalling pathway are worthy of further exploration.

2022-02-17 | PXD026437 | Pride

Multi-omics evaluation of SARS-CoV-2 infected mouse lungs reveals dynamics of host responses

Project description:The outbreak of Coronavirus disease 2019 (COVID-19) throughout the world has caused millions of death, while the dynamics of host responses and the underlying regulation mechanisms during SARS-CoV-2 infection are not well depicted. Lung tissues from a mouse model sensitized to SARS-CoV-2 infection were serially collected at different time points for evaluation of transcriptome, proteome and phosphoproteome. We showed the ebb and flow of several host responses in the lung across viral infection. The signaling pathways and kinases regulating networks were alternated at different phases of infection. Our study not only revealed the dynamics of lung pathophysiology and their underlying molecular mechanisms during SARS-CoV-2 infection, but also highlighted some molecules and signaling pathways that might guide future investigations on COVID-19 therapies.

2022-04-01 | PXD031574 | Pride

Quantitative Proteome and Lysine Lactylome of Proteins within Pathological Site of Rotator Cuff Tendinopathy

Project description:Lysine lactylation (Kla) is a newly discovered posttranslational modification showing the addition of an L-lactate-derived lactyl group to the lysine residue. Histone lactylation has been found to regulate the downstream genes expression involved in the process of infection clearance, homeostasis retore, and tumorigenesis. Like other metabolite mediated PTMs, which the cellular levels of these metabolites affect the stoichiometry of the corresponding PTMs, the level of Kla also responds to the intracellular lactate concentration in a dose-dependent fashion associated with glycolysis metabolism. It has long been noted that manipulation of glycolysis metabolism could affect the tendon cell function, tendon homeostasis, and healing process of tendon.Nonetheless, the lactylation sites and regulations in tendinopathy remain unexplored.

2023-05-10 | PXD033146 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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