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ProteomicsMSLibrarian: Optimized predicted spectral libraries for DIA proteomics
Data-independent mass spectrometry is the method of choice for deep, consistent and accurate single-shot profiling in bottom-up proteomics. While classic workflows required auxiliary DDA-MS analysis of subject samples to derive prior knowledge spectral libraries for targeted quantification from DIA-...
ORGANISM(S): Mus musculus (Mouse) Saccharomyces cerevisiae (Baker's yeast) 
2022-01-17 | PXD028901 | Pride
Q-exactive Predicted spectral library Dia Hf-x Lfq bench 
ProteomicsDopamine transporter and synaptic vesicle sorting defects underlie auxilin-associated Parkinson’s disease
Auxilin participates in the uncoating of clathrin-coated vesicles (CCVs), thereby facilitating synaptic vesicle (SV) regeneration at presynaptic sites. Auxilin (DNAJC6/PARK19) loss-of-function mutations cause early-onset Parkinson’s disease (PD). Here, we utilized auxilin-knockout (KO) mice to eluci...
ORGANISM(S): Mus musculus (Mouse) 
2023-02-16 | PXD040141 | Pride
Dorsal striatum Substantia nigra Endolysosomal system Dopamine Α-synuclein Clathrin coated vesicles Synaptic autophagy Clathrin mediated endocytosis Axonal deformity Lewy bodies L-dopa 
ProteomicsSingle-cell transcriptomic and proteomic analysis of Parkinson’s disease brains
Parkinson’s disease (PD) is a common neurodegenerative disorder where recent evidence suggests may be mediated by inflammatory processes. The molecular architecture of the disease remains to be elucidated. We performed single-nucleus transcriptomics and unbiased proteomics using postmortem tissue ob...
ORGANISM(S): Homo sapiens (Human) 
2024-09-11 | PXD030142 | Pride
Post-mortem brain tissue Parkinson's disease Prefrontal cortex 
ProteomicsSnap-heated freeze-free preservation and processing of the urine proteome
New method for urine proteome preservation and processing based on thermal stabilization and FASP digestion. Four urine proteomes were preserved during 48 h and 6 months using (i) the classic freeze preservation at -20 °C, (ii) snap-heated freeze-free preservation at laboratory temperature (20 °C) a...
ORGANISM(S): Homo sapiens (Human) 
2020-01-10 | PXD012880 | Pride
Stabilizor-based technology Lc-msms Human urine Fasp Proteome preservation 
ProteomicsPtCaf1 interacted proteins in EV and PtGTSF1 KD of Paramecium tetraurelia
The DNA fragment of PtCAF1, one of the core component of PRC2, is fused with FlagHA and transformed into the macronuclear of Paramecium tetraurelia. The interacted proteins of PtCaf1 in Empty vector (EV) control and PtGTSF1 silenced cells were immunoprecipitated with anti-HA antibody, followed with ...
ORGANISM(S): Paramecium tetraurelia 
2025-05-07 | PXD054662 | Pride
Paramecium tetraurelia Ptgtsf1 Prc2 
ProteomicsMytho, An Uncharacterized Gene that Controls Longevity and WIPI2-dependent Autophagy
The identification of genes that confer either extension of life span or accelerate age-related decline was a step forward in our understanding the mechanisms of senescence and revealed that aging process is partially controlled by genetics and transcriptional programs. Here we identified that the u...
ORGANISM(S): Homo sapiens (Human) 
2024-07-02 | PXD022180 | Pride
Wipi2 Autophagy Longevity Mytho 
ProteomicsPerformance Characteristics of Zeno Trap Scanning DIA for Sensitive and Quantitative Proteomics at High Throughput
Proteomic experiments, particularly those addressing dynamic proteome properties, time series, or genetic diversity, require the analysis of large sample numbers. Despite significant advancements in proteomic technologies in recent years, further improvements are needed to accelerate measurement and...
ORGANISM(S): Homo sapiens (Human) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2026-01-19 | PXD063462 | Pride
ProteomicsProtein composition of cobweb spiders gumfoot glue droplets
Orb weavers place aggregate glue on a stretchy capture spiral, whereas cobweb weavers add it to the ends of strong, stiff fibers, called gumfoot lines. We describe the quantitative proteomics of the aggregate glues of two cobweb weaving species, the Western black widow, Latrodectus hesperus, and the...
ORGANISM(S): Latrodectus hesperus (Western black widow spider) Parasteatoda tepidariorum 
2022-02-17 | PXD025685 | Pride
Spider Theridiaadae Glue 
ProteomicsOXSR1 inhibits inflammasome activation by limiting potassium efflux during mycobacterial infection
Pathogenic mycobacteria inhibit inflammasome activation as part of their pathogenesis. While it is known that potassium efflux is a trigger for inflammasome activation, the interaction between mycobacterial infection, potassium efflux and inflammasome activation has not been investigated. Here we us...
ORGANISM(S): Homo sapiens (Human) Mycobacterium marinum 
2022-05-05 | PXD030631 | Pride
Human Mycobacterium Lcms Cell lines 
ProteomicsSOS Genes Are Rapidly Induced While Mutagenesis Is Temporally Regulated by Changes in Protein Activation and Nucleotide Pools After a Sub-lethal Dose of Ciprofloxacin in Escherichia coli
The DNA damage inducible SOS response in bacteria serves to increase survival of the species. The SOS response first initiates error-free repair which is followed by error-prone repair. Here, we have employed a multi-omics approach to elucidate the temporal coordination of the SOS response using tra...
ORGANISM(S): Escherichia coli 
2024-03-26 | PXD047394 | Pride
Signalomics Escherichia coli Ciprofloxacin Sos response 
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