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MetabolomicsIntegrated Analysis of Gut Microbiota, Serum Metabolomics, and Proteomics Reveals Novel Associations With Clinical Symptoms in Patients With Cerebral Infarction
Cerebral infarction (CI) is a major cause of adult disability and mortality worldwide. Mounting evidence supports the critical role of the gut–brain axis in cerebrovascular disease progression. This study aimed to characterize the alterations in gut microbiota, serum metabolome, and serum proteome i...
2026-05-08 | MTBLS14356 | MetaboLights
UnknownAnalysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform.
Not available
S-EPMC10338508 | biostudies-literature
UnknownDIA-BERT: pre-trained end-to-end transformer models for enhanced DIA proteomics data analysis.
Not available
S-EPMC11997033 | biostudies-literature
GenomicsBenchmarking DIA-type Proteomics Using Large-Scale Inter-Patient Heterogeneity Dataset
Benchmarking Proteomics Quantitation in DIA-type data using real patient material to create a benchmark dataset comprising inter-patient heterogeneity
EGAS00001005589 | EGA
ProteomicsUntargeted data independent acquisition proteomics analysis using Orbitrap mass spectrometers and DIA-Umpire
Untargeted data independent acquisition proteomics analysis using Orbitrap mass spectrometers and DIA-Umpire
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-04-01 | MSV000080875 | MassIVE
ProteomicsDIA-Umpire: comprehensive computational framework for data independent acquisition proteomics
This dataset consists of 44 raw MS files, comprising 27 DIA (SWATH) and 15 DDA runs on a TripleTOF 5600 and of two raw mass spectrometry files acquired on a Q Exactive. The composition of the dataset is described in the manuscript by Tsou et al., titled: "DIA-Umpire: comprehensive computational fra...
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2015-01-21 | PXD001587 | Pride
Swath Dia 
ProteomicsDIA proteomics analysis of FGF2-treated human retinal microvascular endothelial cells
Human retinal microvascular endothelial cells were stimunlated with 0 or 50 ng/ml FGF2 and then applied for DIA proteomics.
ORGANISM(S): Homo sapiens (Human) 
2025-05-07 | PXD055191 | Pride
Endothelial cell dia proteomics fgf2 
ProteomicsExtensive and accurate benchmarking of DIA acquisition methods and softwares using a complex
In order to compare workflows for acquisition and treatment of proteomic data analyzed in Data Independent Acquisition (DIA) mode, a proteomic standard has been generated by spike-in the 48 human proteins of UPS1 (Sigma) in a whole cell extract of E.coli at 8 different concentrations ranging from 0....
ORGANISM(S): Escherichia Coli (ncbitaxon:562) Homo Sapiens (ncbitaxon:9606) 
2021-06-09 | MSV000087597 | MassIVE
ProteomicsLocalisation of Organelle Proteins using Data-Independent Acquisition (DIA-LOP)
Subcellular localisation within the proteome fundamentally influences cellular processes, however the development of high-throughput techniques to allow proteome-wide mapping of the cell has proven difficult. Here we present DIA-LOP, an approach capable of high-throughput spatial proteome mapping wi...
ORGANISM(S): Homo sapiens (Human) 
2025-09-29 | PXD063082 | Pride
Human Lc-msms Dia Diapasef Dda 
UnknownRapid and In-Depth Coverage of the (Phospho-)Proteome With Deep Libraries and Optimal Window Design for dia-PASEF.
Not available
S-EPMC9465115 | biostudies-literature
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