Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparison of DDA (Orbitrap Exploris 480) and DIA (timsTOF Pro 2) phosphoproteomics

ABSTRACT: In this experiment, 3 replicate phosphopeptide enrichments using titanium dioxide spin tips (GL Science) of the filamentous fungus Magnaporthe oryzae were measured on a) Orbitrap Exploris 480 in DDA and b) timsTOF Pro 2 in DIA for comparison of model/acquisition type differences.

ORGANISM(S): Cellular Organisms

SUBMITTER: Thomas Michna

PROVIDER: PXD038605 | JPOST Repository | Thu Apr 13 00:00:00 BST 2023

REPOSITORIES: jPOST

ACCESS DATA

Json Xml

Publications

Data-Independent Acquisition (DIA) Is Superior for High Precision Phospho-Peptide Quantification in <i>Magnaporthe oryzae</i>.

Bersching Katharina K Michna Thomas T Tenzer Stefan S Jacob Stefan S

Journal of fungi (Basel, Switzerland) 20221231 1

The dynamic interplay of signaling networks in most major cellular processes is characterized by the orchestration of reversible protein phosphorylation. Consequently, analytic methods such as quantitative phospho-peptidomics have been pushed forward from a highly specialized edge-technique to a powerful and versatile platform for comprehensively analyzing the phosphorylation profile of living organisms. Despite enormous progress in instrumentation and bioinformatics, a high number of missing va ...[more]

PMID: 36675884

Similar Datasets

dia-PASEF HeLa dilution series 0.2ng - 200ng on Bruker timsTOF Pro 2

Project description:Different sample preparation methods were tested for HeLa proteome analysis. A sample obtained using sodium deoxycholate-based lysis allowed identification of the highest number of proteins. For this sample, a dilution series was acquired in triplicates ranging from 0.2ng to 200ng. All measurements were performed on Bruker timsTOF Pro 2 operated in dia-PASEF mode and analysed library-free using DIA-NN 1.8.

2022-06-20 | PXD029836 | Pride

LC-MS/MS interactomics analysis of Praf2 with timsTOF Pro

Project description:LC-MS/MS interactomics analysis of Praf2 using TurboID with timsTOF Pro.

2023-12-20 | PXD029019 | Pride

Epigenomic effect of talc particles on macrophages

Project description:Our objective was to investigate epigenomic and transcriptomic changes in J774 macrophages after incubation with talc and titanium dioxide particles. This dataset comprises the results of reduced representation bisulfite sequencing (RRBS) of the J774 cell DNA 24 hours after exposure to 10 ug/well of fine-sized talc or titanium dioxide particles in vitro with or without 2 ug/mL 17-b estradiol.

2020-05-12 | GSE150322 | GEO

Investigation of Alterations in Gene Expression in the Retina Induced by Intravitreal Injection of titanium dioxide nanoparticles

2013-07-20 | GSE49048 | GEO

Investigation of Alterations in Gene Expression in the Retina Induced by Intravitreal Injection of titanium dioxide nanoparticles

Project description:In this study, we investigated the safety of locally delivered titanium dioxide nanoaprticles at the level of gene expression in the retina. To figure out any definite dose-dependent effect, we injected titanium dioxide nanoparticles into the vitreous cavity of 8-week-old male C57BL/6 mice at the concentration of presumptive therapeutic concentration (PTC; 130.47 ng/ml) and 10 times PTC (1.30 Î¼g/ml). We intravitreally injected PBS or titanium dioxide nanoparticles into the right eyes of 8-week-old male C57BL/6 mice (n = 12 per group). PBS-treated mice were regarded as negative control. Four retinal tissues were pooled into 1 test tube and prepared for further analyses.

2013-07-20 | E-GEOD-49048 | biostudies-arrayexpress

The RNA methylation level of A549 was altered by nanomaterial incubation.

Project description:We reported changes in RNA methylation levels in A549 cells caused by black phosphorus quantum dots and titanium dioxide nanoparticles.

2023-10-21 | GSE159776 | GEO

Pimephales promelas

Project description:Titanium dioxide nanoparticles exposure

| PRJNA119969 | ENA

Impact of the Identification Strategy on the Reproducibility of the DDA and DIA Results.

Project description: Not available

| S-EPMC7898222 | biostudies-literature

PASEF technology on timsTOF Pro improves quality of FPOP analysis

Project description:Fast photochemical oxidation of proteins (FPOP) is a modern technique for studying protein folding, conformations, interactions, etc. In this work, timsTOF Pro mass spectrometer coupled with trapped ion mobility spectrometry was used for identification of oxidative modifications in a model protein. Multiple modifications on the same residues, including six modifications of histidine, were successfully resolved. Moreover, PASEF technology allows successful sequencing even minor populations of modified peptides.

2021-06-10 | PXD020509 | Pride

Oxonium Ion-Guided Ion Mobility-Assisted Glycoproteomics on the timsTOF Pro

Project description:Spatial separation of ions in the gas-phase, providing information about their size as collisional cross-sections, can readily be achieved through ion mobility. The timsTOF Pro combines a trapped ion mobility device with a quadrupole, collision cell and a time-of-flight analyser to enable the analysis of ions at great speed. Here, we show that the timsTOF Pro is capable of physically separating N-glycopeptides from non-modified peptides and producing high-quality fragmentation spectra, both beneficial for glycoproteomics analyses of complex samples. The glycan moieties enlarge the size of glycopeptides compared to non-modified peptides, yielding a clear cluster in the mobilogram that, next to increased dynamic range from the physical separation of glycopeptides and non-modified peptides, can be used to make an effective selection filter for directing the mass spectrometer to analytes of interest. This new approach was applied to selected glycoproteins, human plasma- and neutrophil-derived glycopeptides. We show that the achieved physical separation, combined with the focussing of the mass spectrometer, allows for improved extraction of information from the samples, even at shorter LC gradients of 15 min. We validated our approach on human neutrophil and plasma samples of known make-up, in which we captured the anticipated glycan heterogeneity (paucimannose, phosphomannose, high mannose, hybrid and complex glycans) from diverse biological samples (plasma and neutrophils) at the expected abundances. As the method is compatible with off-the-shelve data acquisition routines and data analysis software, it can readily be applied by any laboratory with a timsTOF Pro and is reproducible as demonstrated by an inter-laboratory comparison between two laboratories.

2023-01-17 | PXD034845 | 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