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ProteomicsProteomic dissection of nanoparticle-containing vesicles reveals a major role for a macropinocytic-like uptake mechanism and multivesicular bodies during intracellular nanoparticle trafficking
Rational design of nanocarriers for drug delivery approaches requires an unbiased knowledge of uptake mechanisms and intracellular trafficking pathways. Here we dissected these processes using a quantitative proteomics approach. We isolated intracellular vesicles containing superparamagnetic iron ox...
ORGANISM(S): Homo sapiens (Human) 
2014-09-25 | PXD001175 | Pride
Human Hdmse Dia Intracellular trafficking Hela Synapt g2s Nanoparticles Endosomes Vesicles 
ProteomicsBenchmarking label-free quantification based on data-independent acquisition (DIA) workflows
Label-free quantification based on data-independent acquisition (DIA) workflows is increasingly popular. Several software tools have been recently published or are commercially available. The present study focuses on the critical evaluation of three different software packages (Progenesis, synapter ...
ORGANISM(S): Homo sapiens (Human) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2017-04-06 | PXD001240 | Pride
Human Yeast E.coli 
ProteomicsEffects of chronic social stress on mitochondrial and mitochondrial-associated membrane protein networks in the mouse brain
Stressors challenge metabolic processes to adapt to ever-changing environmental conditions and herein, the brain is exceptionally amenable to change. Simultaneously, the high cerebral energy demands may render the brain particularly vulnerable to the metabolic consequences of psychological stress. M...
ORGANISM(S): Mus musculus (Mouse) 
2022-10-13 | PXD015983 | Pride
Mitochondrial-associated membrane Brain Mouse Chronic stress 
ProteomicsIdentification of kinase activity in ischemic heart disease
We performed discovery proteomics and phosphoproteomics analysis of human heart tissue to identify possibly hyperactive pathways in ischemic heart disease.
ORGANISM(S): Homo sapiens (Human) 
2023-03-11 | PXD024727 | Pride
Phosphoproteomics Map kinase activity Myeloid cell coagulation Ischemic heart disease 
ProteomicsLFQbench enables a multi-centered benchmark study demonstrating robust proteomic label-free quantification
The consistent and accurate quantification of proteins is a challenging task for mass spectrometry (MS)-based proteomics. SWATH-MS uses data-independent acquisition (DIA) for label-free quantification. Here we evaluated five software tools for processing SWATH-MS data: OpenSWATH, SWATH2.0, Skyline, ...
ORGANISM(S): Escherichia Coli (ncbitaxon:562) Homo Sapiens (ncbitaxon:9606) Saccharomyces Cerevisiae (ncbitaxon:4932) 
2017-04-27 | MSV000081024 | MassIVE
ProteomicsLC-MS confirmation of alternative YPD1 isoforms from Magnaporthe oryzae
This project aims to understand better the stress response mechanisms of components of the well known High Osmolarity Glycerol two-component regulatory system in the model organism Magnaporthe oryzae. Currently, two putative isoforms of the transfer protein YPD1 (MGG_07173) are described as theoreti...
ORGANISM(S): Pyricularia oryzae 70-15 
2021-09-10 | PXD024832 | Pride
In-gel digest Lc-ms/ms Ypd1 Isoform identification Alternative splicing Magnaporthe oryzae 
ProteomicsK2P2.1 shapes morphology and function of brain endothelial cells via actin network remodeling
K2P2.1 (gene: Kcnk2), a two-pore domain potassium channel, is an important regulator of leukocyte transmigration across the blood-brain barrier. However, the underlying molecular mechanisms remain poorly characterized. We here show that Kcnk2-/- mouse brain microvascular endothelial cells (MBMECs) s...
ORGANISM(S): Mus musculus (Mouse) 
2025-07-28 | PXD031051 | Pride
Actin remodeling Eae Kcnk2 Blood-brain-barrier Trek1 K2p2.1 Lc-ms/ms 
ProteomicsUnbiased proteomic analysis of postsynaptic density fractions from Shank3 mutant mice reveals brain region specific changes highly relevant to autism spectrum disorder
Disruption of the human SHANK3 gene can cause several neuropsychiatric disease entities including Phelan-McDermid syndrome (PMS), autism spectrum disorders (ASDs) and intellectual disability (ID). Although a wide array of neurobiological studies strongly supports a major role for SHANK3 in organizin...
ORGANISM(S): Mus musculus (Mouse) 
2017-03-08 | PXD005192 | Pride
Shank3 mutants Proteomics Hippocampus Striatum Postsynaptic density (psd) 
ProteomicsHybrid label-free quantification proteomics and QconCAT-assisted quantification of amylase-trypsin inhibitors from flours of 150 wheat varieties (3 field locations) by LC-MSE
Wheat (Triticum aestivum ssp. aestivum) contributes to 20% of the human protein supply, delivers essential amino acids and is of fundamental importance for bread and pasta quality. Wheat proteins are also involved in adverse human reactions like celiac disease, wheat allergy and the non-celiac wheat...
ORGANISM(S): Triticum aestivum (Wheat) 
2021-09-10 | PXD023654 | Pride
Mse Breeding Amylase-trypsin inhibitors (atis) Synapt g2-s Proteomics Wheat varieties Qconcat Label-free quantification (lfq) Non-celiac wheat sensitivity (ncws) Data-independent acquisition (dia) 
ProteomicsPost-column solvent addition enhances sensitivity of microflow-based bottom-up proteomics
We demonstrate that post-column addition of organic solvents leads to a strong enhancement of electrospray stability in microflow LC-MS experiments improving the sensitivity across the entire gradient, for early eluting peptides by up to tenfold. Post-column solvent addition did not negatively affec...
ORGANISM(S): Homo sapiens (Human) 
2019-05-28 | PXD011970 | Pride
Post-column solvent addition Hela digest Microflow lc-ms Bottom-up proteomics 
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