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ProteomicsImproving Precursor Selectivity in Data Independent Acquisition Using Overlapping Windows
A major goal of proteomics research is the accurate and sensitive identification and quantification of a broad range of proteins within a sample. Data Independent Acquisition (DIA) approaches that acquire MS/MS spectra independently of precursor information have been developed to overcome the reprod...
ORGANISM(S): Bos Taurus Saccharomyces Cerevisiae 
2019-02-02 | PXD011910 | panorama
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 
ProteomicsProteome study to optimize Zeno SWATH DIA
Data-independent acquisition (DIA) techniques, such as SWATH acquisition, have emerged as the preferred strategy for proteomic analysis. Our study optimizes the SWATH-DIA method using a narrow isolation window placement approach improving its proteomic performance. We optimized the acquisition param...
ORGANISM(S): Homo Sapiens (human) Cellular Organisms Mus Musculus (mouse) 
2024-07-20 | PXD050030 | JPOST Repository
GenomicsFormaldehyde-assisted isolation of regulatory elements with next generation sequencing (FAIRE-seq) in primary human macrophages and foam cells
We report the open chromatin landscape in primary human macrophages and foam cells using FAIRE-seq CD14+ monocytes were isolated from the blood of 3 healthy volunteers. Monocytes were differentiated into macrophages by culture for 7 days with 50ng/ml macrophage colony stimulating factor and then tre...
ORGANISM(S): Homo sapiens 
2015-04-08 | E-GEOD-54971 | biostudies-arrayexpress
ProteomicsAn updated perspective on deconvoluting chimeric MS/MS spectra by LC and precursor isolation and their subsequent assignment by the CharmeRT mPSM search strategy
Considering the recent advances in LC and mPSM methodologies, we aimed to provide a systematic comparison and in-depth analysis of the effects that standard and specialized LC setups, as well as different isolation windows, have on the occurrence and assignment of chimeric spectra derived from a com...
ORGANISM(S): Homo sapiens (Human) 
2019-05-20 | PXD012635 | Pride
Liquid chromatography Tandem mass spectrometry Chimeric spectra Isolation interference 
UnknownImproving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows.
Not available
S-EPMC6445824 | biostudies-literature
ProteomicsThe Q Exactive HF, a Benchtop Mass Spectrometer with a Pre-filter, High Performance Quadrupole and an Ultra-High Field Orbitrap Analyzer
The quadrupole Orbitrap mass spectrometer (Q Exactive) has made a powerful proteomics instrument available in a benchtop format. It significantly boosted analyzable proteins per hour and has now evolved into a proteomics analysis workhorse for many laboratories. Here we describe the Q Exactive Plus ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-04-01 | MSV000080865 | MassIVE
ProteomicsA comparative proteomic, transcriptomic and glycomic analysis of extracellular vesicle isolation techniques highlights ExoGAG efficiency for a more complete identification of breast milk molecular signaling pathways
Background: Human milk (HM) is the earliest form of extrauterine communication between mother and infant. We recently showed a functional characterization of HM, unmasking the molecular mechanisms related to EV signaling and its functional role in prematurity. In that study, we identified the need t...
ORGANISM(S): Homo sapiens (Human) 
2025-10-13 | PXD060683 | Pride
Glycomics. Proteomics Extracellular vesicles Human milk Transcriptomics Isolation method 
ProteomicsA PEROXO-Tag enables rapid isolation of peroxisomes from human cells
Peroxisomes are metabolic organelles that perform a diverse array of critical functions in human physiology. Traditional isolation methods for peroxisomes can take more than one hour to complete and can be laborious to implement. To address this, we have now extended our prior work on rapid organell...
ORGANISM(S): Homo sapiens (Human) 
2020-05-20 | PXD018880 | Pride
Human hek-293t Peroxisome Peroxo-ip 
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
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