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MetabolomicsComparison of Full-Scan, Data-Dependent, and Data-Independent Acquisition Modes in Liquid Chromatography-Mass Spectrometry Based Untargeted Metabolomics
Full-scan, data-dependent acquisition (DDA), and data-independent acquisition (DIA) are the three common data acquisition modes in high resolution mass spectrometry-based untargeted metabolomics. It is an important yet underrated research topic on which acquisition mode is more suitable for a given ...
2020-05-21 | MTBLS1572 | MetaboLights
MetabolomicsLiquid Chromatography-Mass Spectrometry Quantification of Phytochemicals in Withania somnifera Using Data-Dependent Acquisition, Multiple-Reaction-Monitoring, and Parallel-Reaction-Monitoring with an Inclusion List

Characterization of botanical extracts by mass spectrometry-based metabolomics analysis helps in determining the phytochemical composition that underlies their bioactivity and potential health benefits, while also supporting reproducibility of effects in clinical trials. The quantification of sev...

2024-07-10 | MTBLS10418 | MetaboLights
MetabolomicsEvaluation of significant features discovered from different data acquisition modes in mass spectrometry-based untargeted metabolomics

Despite the growing popularity of liquid chromatography-mass spectrometry (LC-MS)-based metabolomics, no study has yet to systematically compare the performance of different data acquisition modes in the discovery of significantly altered metabolic features, which is an important task of untarget...

2020-10-02 | MTBLS1842 | MetaboLights
MetabolomicsDIAMetAlyzer allows automated false-discovery rate-controlled analysis for data-independent acquisition in metabolomics
The extraction of meaningful biological knowledge from high-throughput mass spectrometry data relies on limiting false discoveries to a manageable amount. For targeted approaches in metabolomics a main challenge is the detection of false positive metabolic features in the low signal-to-noise ranges ...
2022-09-05 | MTBLS1108 | MetaboLights
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
MetabolomicsClostridium bolteae suppresses Enterobacteriaceae expansion and restores gut microbiome homeostasis via disrupting siderophore-mediated iron acquisition

Intestinal inflammation and the related gut microbiome dysbiosis are becoming prevalent worldwide. Overgrowth of Enterobacteriaceae exacerbates intestinal inflammation and gut microbiome dysbiosis. Enterobacteriaceae secrets siderophore to acquire iron and survive in the iron-limited gut. Therefo...

2026-01-03 | MTBLS13592 | MetaboLights
MetabolomicsDIATAGeR: Triacylglycerol Annotation of Data-Independent Acquisition based Lipidomics

Triacylglycerols (TGs) are the most abundant lipids in the human body and the primary source of energy storage. Altered TGs are implicated in metabolic syndrome and detailed structural information may provide novel insights into diseases pathology. TGs are comprised of three fatty acyls with vari...

2025-03-04 | MTBLS11927 | MetaboLights
ProteomicsA Data-Dependent Acquisition Ladder for Ultrasensitive (Neuro)Proteomics
We report here a data acquisition strategy that expands the detectable and quantifiable proteome from trace amounts of protein digests using microanalytical capillary electrophoresis (µCE) electrospray ionization (ESI) high-resolution mass spectrometry (HRMS). Data-dependent acquisition (DDA) was pr...
ORGANISM(S): Mus musculus (Mouse) 
2022-02-18 | PXD027428 | Pride
Neuron Neuroscience Proteomics Mouse. Mass spectrometry Capillary electrophoresis Data dependent acquisition 
ProteomicsA Versatile Isobaric Tag Enables Proteome Quantification in Data Dependent and Data Independent Acquisition Mode
Quantifying proteins based on peptide-coupled reporter-ions is a leading multiplexed quantitative strategy in proteomics that significantly alleviates the problem of ratio distortion caused by peptide co-fragmentation, as commonly observed in other reporter-ion based approaches, such as TMT and iTRA...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2021-09-09 | PXD021187 | Pride
Quantitative proteomics Data dependent acquisition Isobaric labeling Data-independent acquisition 
MetabolomicsWT 2.0: Unveiling the “dark matter” in the metabolome using all-ion stepwise fragmentation acquisition mode (ASFAM) and deep learning-based feature extraction

Current metabolomics methods often miss low-abundance compounds and yield incomplete or ambiguous MS2 spectra, resulting in the presence of “dark matter” within the metabolome. Here, we introduce WT 2.0, which employs an all-ion stepwise fragmentation acquisition mode (ASFAM) to acquire comprehe...

2025-09-23 | MTBLS13023 | MetaboLights
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