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MetabolomicsLipidCreator workbench to probe the lipidomic landscape - Platelet isolation and stimulation - DIA lipid mediator validation

Here we present LipidCreator, a software that fully supports targeted lipidomics assay development. LipidCreator offers a comprehensive framework to compute MS/MS fragment masses for over 60 lipid classes. LipidCreator provides all functionalities needed to define fragments, manage stable isotope...

2020-04-15 | MTBLS1382 | MetaboLights
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
ProteomicsDIA to inform Triple Quad Assay development
Mass spectrometry based targeted proteomics methods provide sensitive and high-throughput analysis of selected proteins. To develop a targeted bottom-up proteomics assay, peptides must be evaluated as proxies for the measurement of a protein or proteoform in a biological matrix. Candidate peptide se...
ORGANISM(S): Homo Sapiens 
PXD059611 | panorama
ProteomicsSimultaneous targeted and discovery-driven clinical proteotyping using hybrid-PRM/DIA
Background MS-based proteotyping has been widely used for biomarker discovery. However, the clinical/translational proteotyping community requires strategies that not only enable the discovery of novel biomarker candidates but also increase the likelihood of establishing these protein-based biomarke...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
MSV000092996 | MassIVE
ProteomicsData-independent Acquisition for the orbitrap. A tutorial.
Data-independent acquisition (DIA) is a powerful mass spectrometric technique to perform both protein identification and quantification of complex protein samples. Setting up DIA methods on Orbitrap analyzers requires a thorough overview over the actions the Orbitrap mass spectrometers carry out. Th...
ORGANISM(S): Pseudomonas Aeruginosa 
2019-08-09 | PXD011449 | JPOST Repository
ProteomicsDIA-enabled discovery of alternative proteins (AltProts) in mouse heart development
In this project, we conducted an evaluation of mass spectrometry methods using mouse heart and HCT116 cell samples. The results demonstrated that the data-independent acquisition (DIA) approach outperformed data-dependent acquisition (DDA) in the identification of Altprot and canonical proteins. Sub...
ORGANISM(S): Mus musculus (Mouse) 
2025-01-17 | PXD045956 | Pride
Altorfs  mouse heart development  mass spectroemtry 
ProteomicsA fully automated FAIMS-DIA mass spectrometry-based proteomic pipeline
Here, we present a standardized, “off-the-shelf” proteomics pipeline working in a single 96-well plate to achieve deep coverage of cellular proteomes with high throughput and scalability. This integrated pipeline streamlining a fully automated sample preparation platform, data independent acquisitio...
ORGANISM(S): Homo sapiens (Human) 
2023-08-22 | PXD029902 | Pride
Dia Ipsc Temporal proteomics Neurodegenerative Single-shot Faims 
MetabolomicsCustomized Consensus Spectral Library Building for Untargeted Quantitative Metabolomics Analysis with Data Independent Acquisition Mass Spectrometry and MetaboDIA Workflow
Data independent acquisition-mass spectrometry (DIA-MS) coupled with liquid chromatography is a promising approach for rapid, automatic sampling of MS/MS data in untargeted metabolomics. However, wide isolation windows in DIA-MS generate MS/MS spectra containing a mixed population of fragment ions t...
2018-03-26 | MTBLS417 | MetaboLights
ProteomicsOcotea dataset project - UNIFAL
60 Ocotea crude plant extracts LC-HRMS/DIA-MSe metabolomics data
ORGANISM(S): Ocotea (ncbitaxon:63801) 
MSV000093006 | MassIVE
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
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