Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

HEK293T_The Label-free DIA-MS nanoproteomics workflow based on empirically corrected spectral library and application for 5000 PBMCs stimulated by LPS

ABSTRACT: A refined HEK293T peptide dilution series acquired in DIA mode on Orbitrap Lumos.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Na Jiang

LAB HEAD: Ruibing Chen

PROVIDER: PXD029738 | Pride | 2022-04-27

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	DIA-NN_noirt_100ng_DDA_report.tsv	Tabular
	DIA-NN_noirt_20ng_DDA_report.tsv	Tabular
	DIA-NN_noirt_4ng_DDA_report.tsv	Tabular
	DIA-NN_noirt_500ng_DDA_report.tsv	Tabular
	DIANN_noirt_100ng_GPF_report.tsv	Tabular

Items per page:

1 - 5 of 78

Similar Datasets

PBMC_A data-independent acquisition (DIA)-based quantification workflow for proteome analysis of 5000 cells

Project description:An optimized workflow for nanoscale proteomics is applied to the proteomics profiling of 5000 PBMCs in DIA mode on Orbitrap Lumos.

2022-04-27 | PXD029721 | Pride

Proteomic analysis of pleomorphic dermal sarcoma

Project description:In this study, we aimed to unravel the molecular underpinnings of pleomorphic dermal sarcomas (PDS), rare skin tumors often seen in sun-exposed regions. Using mass spectrometry, we examined proteomic profiles of 20 samples of normal healthy skin tissue (SNT), 27 malignant melanomas (MM), 20 cutaneous squamous cell carcinomas (cSCC), and 24 PDS. Our analysis aimed to: I.) Determine the potential cell of origin for PDS by correlating protein abundance to tumor purity using both RNA- and DNA-sequencing data. II.) Investigate receptor/ligand (R/L) interactions and their related pathways, highlighting distinct signaling differences between cSCC, MM, and PDS. III.) Identify differential protein markers, such as MAP1B_HUMAN, that can distinguish between cSCC, MM, and PDS. IV.) Explore proteins linked to immunosuppression in PDS, with a focus on those related to the negative regulation of interferon-gamma signaling. Together, this comprehensive proteomic exploration provides valuable insights into PDS and potential therapeutic targets.

2024-06-16 | PXD046388 | Pride

Gut bacterial phytohormone modulates olfactory sensing, chemotaxis and mortality in fruit fly (Drosophila melanogaster): a new dimension to gut-brain axis

Project description:Aim of the study was to profile and quantify the proteins head region of D. melanogaster that are changing as a result of phytohormone administration. Data-independent acquisition (DIA) bases quantitative proteomics approach were used to achieve this aim. An Orbitrap Fusion Tribrid mass spectrometer (Thermo Fischer Scientific, Bremen, Germany) connected to the Easy- nLC-1200 nanoflow liquid chromatography system (Thermo Scientific) was used for data acquisition.

2024-05-22 | PXD044924 | Pride

Global proteome of Atg5flox:Slc32a1-Cre:tdTomato FACS sorted WT and KO neurons

Project description:The experiment was performed to identify autophagy targets in wildtype and autophagy-deficient forebrain inhibitory neurons. Therefore, neurons were isolated from the cortex, hippocampus and striatum of 2-3 weeks old Atg5flox/flox:Slc32a1-Cretg/wt:tdTomato+ (KO) and Atg5wt/wt:Slc332a1-Cretg/wt:tdTomato+ (WT) mice. Neurons in suspension were FACS sorted and inhibitory forebrain neurons expressing tdTomato were forwarded to global proteome analysis assessed by LC-MS/MS.

2022-11-15 | PXD031535 | Pride

Benchmarking DIA data analysis workflows

Project description:Data independent acquisition (DIA) has become a well-established method in LC-MS driven proteomics. Nonetheless, there are still a lot of possibilities at the data analysis level. By benchmarking different DIA analysis workflows through a ground truth sample mimicking real differential abundance samples, consisting of a differential spike-in of UPS2 in a constant yeast background, we provide a roadmap for DIA data analysis of shotgun samples based on whether sensitivity, precision or accuracy is of the essence. Three different commonly used DIA software tools (DIA-NN, EncyclopeDIA and SpectronautTM) were tested in both spectral library mode and spectral library free mode. In spectral library mode we used the independent spectral library prediction tools Prosit and MS2PIP together with DeepLC, next to the classical DDA-based spectral libraries. In total we benchmarked 12 DIA workflows. DIA-NN in library free mode or using in silico predicted libraries shows the highest sensitivity maintaining a high reproducibility and accuracy.

2024-05-06 | PXD044981 | Pride

The fitness cost of spurious phosphorylation

Project description:The fidelity of signal transmission requires the binding of regulatory molecules to their cognate targets. However, the crowded cell interior risks off-target interactions between proteins that are functionally unrelated. Understanding the constraints this imposes on cell systems evolution requires the fitness cost of spurious interactions to be quantified. Towards this end, we express human tyrosine kinases in the budding yeast S. cerevisiae. Yeast lacks bona fide tyrosine kinases and so the majority of resulting pY sites are functionless and artificial. We express 24 unique tyrosine kinases in total and perform phosphoproteomics in each case, resulting in ~30,000 phosphosites sites mapping to 3500 phosphoproteins. Examination of the fitness costs in each strain reveals a strong correlation between the number of spurious pY sites generated and negative effects on growth. Moreover, the prediction of pY effects on protein structure and on protein function (conservation-based) reveals potential for the widespread perturbation of the yeast proteome. Comparing the spurious pY sites (pre-selection) with native pY sites in human (post-selection) also demonstrates the recurrent modification of proteins and sites with no homology to native substrates. However, examination of these data together (fitness and phosphoproteomics) strongly suggests that a large number of the pY sites generated have a negligible effect on fitness. Finally, we test the hypothesis of pY counter-selection following the emergence of tyrosine kinases in metazoan species, but find no strong evidence for proteome-wide selection against spurious Y phosphorylation.

2024-09-12 | PXD045466 | Pride

FAS Inhibited Proteomics and Phosphoproteomics Profiling of Colorectal Cancer Spheroids shows Activation of Ferroptotic Death Mechanism

Project description:Colorectal cancer (CRC) is projected to become the third most diagnosed and third most fatal cancer in the United States by 2024, with early onset CRC on the rise. Research is constantly underway to discover novel therapeutics for the treatment of various cancers to improve patient outcomes and survival rates. Recently, fatty acid synthase (FAS) has become a druggable target of interest for the treatment of many different cancers. FAS inhibitors have been developed over the years with mixed success. One such inhibitor, TVB-2640, has gained popularity for its high specificity for FAS and has even entered a phase 1 clinical trial for the treatment of solid tumors. However, the distinct molecular differences that occur upon inhibiting FAS have yet to be understood. Here, we conduct time course proteomics and phosphoproteomics on analyses HCT 116 and HT-29 CRC spheroids inhibited with either a generation 1 (cerulenin) or generation 2 (TVB-2640) FAS inhibitor. Proteins involved in lipid metabolism and cellular respiration were altered in abundance. It was also observed that proteins and enzymes involved in ferroptosis—an iron mediated form of cell death—were altered. These results show HT-29 spheroids exposed to cerulenin or TVB-2640 are undergoing a ferroptotic death mechanism.

2024-08-10 | PXD050987 | Pride

Myeloperoxidase is a Critical Mediator of Anthracycline-induced Cardiomyopathy

Project description:The anthracycline doxorubicin is a commonly used chemotherapeutic drug that induces cardiomyopathy in almost 10% of patients. The aim of this study was to examine the role of the leukocyte-derived enzyme Myeloperoxidase (MPO) in pathogenesis of anthracycline-induced Cardiomyopathy (AICM). We performed proteomics on whole heart tissue of MPO-deficient mice on C57BL/6J background and wildtype (WT) littermates seven days after intravenous injection of the anthracycline Doxorubicin (20 mg/kg bodyweight, dissolved in saline) or saline (NaCl).

2023-08-30 | PXD037524 | Pride

Mapping perturbations in the cellular proteome of OCIAD1 and OCIAD2 knockdown U2OS cells.

Project description:To gain insight into the function of both OCIAD paralogs, we used untargeted quantitative mass spectrometry to compare the whole-cell proteomes of control U2OS cells, U2OS cells with individual or double OCIAD1/OCIAD2 knockdown, and OCIAD1 knockdown cells in which OCIAD1 expression was reintroduced by lentiviral delivery.

2021-05-14 | PXD025573 | Pride

Mapping the interactome of OCIAD1 in human K562 cells

Project description:Immunoprecipitation of OCIAD1 followed by mass spectrometry analysis to identify binding partners in human cells. To determine the functional significance of OCIAD1 interactors, we also looked for interactions that were modulated by a loss-of-function mutant (F102A).

2021-05-14 | PXD025682 | 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