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MetabolomicsLipidCreator workbench to probe the lipidomic landscape - Platelet isolation and stimulation, Targeted Phospho and Glycerolipid Profiling

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 | MTBLS1369 | MetaboLights
ProteomicsBenchmarking CHIMERYS using Wide Window Acquisition and Classical Narrow Isolation Window Data Dependent Acquisition
A comprehensive proteome map is essential to elucidate molecular pathways and protein functions. Although great improvements in sample preparation, instrumentation and data analysis already yield-ed impressive results, current studies suffer from a limited proteomic depth and dynamic range there-for...
ORGANISM(S): Mus musculus (Mouse) Homo sapiens (Human) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2024-02-13 | PXD045500 | Pride
E. coli Wide window acquisition Yeast Direct injection Micropillar array chromatography Vanquish neo Hela Orbitrap exploris 480 Single cells Trap-and-elute 
ProteomicsIsolation window optimization using predicted libraries for deep and accurate proteome profiling by data-independent acquisition
In silico spectral library prediction of all possible peptides from whole organisms has a great potential for improving proteome profiling by data-independent acquisition and extending its scope of application. In combination with other recent improvements in the field, including sample preparation,...
ORGANISM(S): Candida albicans (Yeast) Homo sapiens (Human) Escherichia coli Staphylococcus aureus 
2020-08-25 | PXD017639 | Pride
Isolation window Predicted spectral library Speed Quantitative proteomics Data-independent acquisition 
ProteomicsNarrow-window DIA: Ultra-fast quantitative analysis of comprehensive proteomes with high sequencing depth. Evaluation of window width and injection time.
Mass spectrometry (MS)-based proteomics aims to characterize comprehensive proteomes in a fast and reproducible manner. Here, we present an ultra-fast scanning data-independent acquisition (DIA) strategy consisting on 2-Th precursor isolation windows, dissolving the differences between data-dependen...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
MSV000095977 | MassIVE
TranscriptomicsSperm RNA: A window to idiopathic infertile couples
We examine how NGS sequencing of sperm can provide a window as to how particular perturbations of the sperm RNA profile from baseline may be indicative of male factor infertility, and may thus provide direction as to proper course of infertility treatment for couple. NGS RNA-seq of 72 sperm samples ...
ORGANISM(S): Homo sapiens 
2015-07-09 | E-GEOD-65683 | biostudies-arrayexpress
ProteomicsDecoding the impact of isolation window selection and QuantUMS filtering in DIA-NN for DIA quantification of peptides and proteins.
Proteomic studies using Data Independent Acquisition (DIA) have gained momentum in all fields of biology. Search engines are evolving to keep up with the latest developments in instrument technology. DIA-NN is the most popular software for DIA analysis under academic use license. The QuantUMS algori...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2025-12-04 | PXD063416 | Pride
Isolation window Dia Mass spectrometry Quantums Quantification 
UnknownSpatiotemporal isolation of attosecond soft X-ray pulses in the water window.
Not available
S-EPMC4382990 | biostudies-literature
ProteomicsNarrow-window DIA: Ultra-fast quantitative analysis of comprehensive proteomes with high sequencing depth. Evaluation of window width and injection time.
Mass spectrometry (MS)-based proteomics aims to characterize comprehensive proteomes in a fast and reproducible manner. Here, we present an ultra-fast scanning data-independent acquisition (DIA) strategy consisting on 2-Th precursor isolation windows, dissolving the differences between data-dependen...
ORGANISM(S): Homo sapiens (Human) 
2024-02-01 | PXD046285 | Pride
Dia Astral Proteomics 
ProteomicsEvaluation of a Dual Isolation Width Acquisition (DIWA) method for isobaric labelling ratio decompression
Stable isotope labelling of peptides using isobaric reagents such as iTRAQ and TMT enables the multiplexed analysis of proteomes with deep quantitative coverage. Isobaric tagging demonstrates high precision but imperfect accuracy due to ratio underestimation caused by co-fragmentation of ions with m...
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2019-01-07 | PXD010571 | Pride
Method development Tmt Msms Diwa 
ProteomicsNo One-Size-Fits-All: Method-Dependent Recovery of Distinct EV Subsets Across 11 Plasma derived EV Isolation Methods
We evaluated eleven EV isolation methods to define their performance charac-teristics and optimal applications. EVs were quantified by NanoFCM, profiled for tetraspanins (CD9, CD63, CD81) via MSD assays, and further characterized by LC-MS/MS proteomics.
ORGANISM(S): Homo sapiens (Human) 
2026-09-14 | PXD075093 | Pride
Reproducibility Extracellular vesicles (evs) Isolation methods Standardization Liquid biopsy Proteomics Biomarkers 
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