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ProteomicsiDIA-QC: AI-empowered Data-Independent Acquisition Mass Spectrometry-based Quality Control
Quality control (QC) in mass spectrometry (MS)-based proteomics is mainly based on data-dependent acquisition (DDA) analysis of standard samples. Here, we collected 2638 files acquired by data independent acquisition (DIA) and paired DDA files from mouse liver digests using 21 mass spectrometers acr...
ORGANISM(S): Mus musculus (Mouse) 
2024-11-08 | PXD052871 | Pride
Quality control  data independent acquistion diapasef 
ProteomicsA comprehensive Proteomic Investigation of Ebf1 Heterozygosity in pro B lymphocytes utilizing Data Independent Acquisition (DIA) and Data Dependent Acquisition (DDA) Approaches
The study provide a comprehensive comparison between data dependent acquistion (DDA) and data independen acquisition (DIA) with the aim to detect and quantify proteome changes associated with reduced gene dosage using Ebf1 transcription factor as a modal.
ORGANISM(S): Mus musculus (Mouse) 
2022-03-21 | PXD006620 | Pride
Spectronaut Trascription factor Maxquant Dia Dda 
ProteomicsRecommendations for Automating Hydrogen/Deuterium Exchange Mass Spectrometry Measurements using Data-Independent Acquisition Methods
Two test HX-DIA datasets, Phosphorylase B kinetics and nanobody binding, that can be used to explore the features of DIA-HX and the AutoHX software.
ORGANISM(S): Homo sapiens (Human) 
2025-01-22 | PXD060028 | Pride
Autohx Data-independent acquistion Hx-ms2 Hydrogen deuterium exchange Hx-dia 
ProteomicsNarrow precursor window for DIA-MS enhances protein identification and quantification
Data independent acquistion (DIA) is becoming widely as a method of choice in quantitation proteomics due to its high reproducibility and quantitation accuracy at high-throughput fashion. In this project, we systematically evaluated the effect of the selected precursor mass range for DIA-MS on the p...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2021-10-01 | PXD026965 | Pride
Arabidopsis Data independent acqusition (dia) Lc-ms/ms 
Proteomics1,4-napthoquinone-sulfomethylene-glucose conjugates, a novel targeted approach for advanced prostate cancer
Rationale: The Warburg effect is a shift from oxidative phosphorylation to aerobic glycolysis accompanied by an enormous increase in glucose uptake into the cancer cell. We have utilized this effect to design a new group of targeted cytotoxic 1,4-naphthoquinones. To optimize the compounds for clinic...
ORGANISM(S): Homo sapiens (Human) 
2025-04-14 | PXD052256 | Pride
1 Castration-resistant prostate cancer Combinational therapy. 4-naphthoquinone Ros Mitochondria Warburg effect Apoptosis 
ProteomicsPREDICTIVE FACTORS FOR PERIOPERATIVE TREATMENTS IN BLADDER CARCINOMA
Muscle-invasive bladder carcinoma (MIBC) has been classified into transcriptomic subtypes, but proteomics studies remain scarce. Fifty-eight paraffin-embedded MIBC samples obtained atransurethral resection (prior to treatment) and at the cystectomy (after neoadjuvant treatment) were analyzed for pro...
ORGANISM(S): Homo sapiens (Human) 
2026-01-19 | PXD057995 | Pride
Muscle-invasive bladder carcinoma Neoadjuvant chemotherapy Data-independent acquistion 
ProteomicsRobust proteome profiling of cysteine-reactive fragments using label-free chemoproteomics - HEK293T - Global expression proteomics
In this manuscript we describe our work on the development of a label-free chemoproteomics screening platform for cysteine reactive covalent fragments on a 96 well plate format. This platform profiles cysteine reactive fragments by competition with the hyper-reactive iodoacetamide desthiobiotin (IA-...
ORGANISM(S): Homo sapiens (Human) 
2024-11-18 | PXD054105 | Pride
Data independant acquistion Label free quantification 
ProteomicsProteomic analysis of bacteria-infected wound tissue in a diabetic mouse model following electrical stimulation therapy delivered by a PMH dressing
In this work, we established a bacteria-infected diabetic mouse model by spraying MRSA bacteria on the wound of diabetic mice, and then used a novel bioelectronic wound dressing to treat the wound, with commercially available Tegaderm film as a control. After 20 days of therapy, we collected wound t...
ORGANISM(S): Mus Musculus 
2023-02-18 | PXD040252 |
ProteomicsMultilayered Omics Revealsl Sex- and Depot-Dependent Adipose Progenitor Cell Heterogeneity
White adipose tissue (WAT) harbors functionally diverse subpopulations of adipose progenitor cells that differentially impact tissue plasticity in a sex- and depot-dependent manner. To date, the molecular basis of this cellular heterogeneity has not been fully defined. Here, we describe a multilayer...
ORGANISM(S): Mus musculus (Mouse) 
2023-03-11 | PXD023829 | Pride
Multilayered omics Adipogenesis Inflammation Preadipocytes Ppar. Adipocyte precursor cells Cellular heterogeneity 
UnknownComparison of data acquisition modes with Orbitrap high-resolution mass spectrometry for targeted and non-targeted residue screening in aquacultured eel.
Not available
S-EPMC7722469 | biostudies-literature
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