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MetabolomicsKnown Metabolite Annotation in Different Biological Samples using Ion Mobility Collision Cross-Section Atlas (AllCCS)

The metabolome includes not just known but also unknown metabolites; however, metabolite annotation remains the bottleneck in untargeted metabolomics. Ion mobility – mass spectrometry (IM-MS) has emerged as a promising technology by providing multi-dimensional characterizations of metabolites. He...

2020-07-28 | MTBLS1693 | MetaboLights
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
GenomicsSemiconductor-based sequencing of genome-wide DNA methylation states
Methylated DNA immunoprecipitation sequencing (MeDIP-Seq) is a widely used approach to study DNA methylation genome-wide. Here, we present a novel MeDIP-Seq protocol compatible with the Ion Torrent semiconductor-based sequencing platform that is scalable and accurately identifies sites of differe...
ORGANISM(S): Homo sapiens 
2015-06-10 | E-GEOD-61968 | biostudies-arrayexpress
ProteomicsAccumulated ion monitoring for improved sensitivity
This work aimed to improve sensitivity of targeted detection by orbitrap mass spectrometers. Co-isolation of contaminant ions was identified as the major factor limiting sensitivity, and LOD of both PRM and accumulated precursor ion scanning (AIM) was improved by increased chromatographic resolution...
ORGANISM(S): Homo sapiens (Human) 
2017-08-24 | PXD006236 | Pride
Quantitative-ms Prm Orbitrap Phosphorylation Targeted-ms 
TranscriptomicsTranscription profiling by array of Enterococcus faecium grown in open circuit (control) and closed circuit (current collection) to observe the difference in extracellular electron transfer (EET) mechanisms.
Enterococcus faecium was grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms. mRNA was extracted, amplified and used on Combimatrix custom arrays to obtain a
ORGANISM(S): Enterococcus faecium 
2010-07-08 | E-MTAB-268 | biostudies-arrayexpress
TranscriptomicsTranscription profiling by array of Pseudomonas aeruginosa was grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms.
Pseudomonas aeruginosa was grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms. mRNA was extracted, amplified and used on Combimatrix custom arrays to obtain
ORGANISM(S): Pseudomonas aeruginosa 
2010-07-08 | E-MTAB-269 | biostudies-arrayexpress
TranscriptomicsTranscription profiling by array of Shewanella oneidensis was grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms.
Shewanella oneidensis was grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms. mRNA was extracted, amplified and used on Combimatrix custom arrays to obtain an expression profile. Analysis was performed...
ORGANISM(S): Shewanella oneidensis 
2010-07-08 | E-MTAB-266 | biostudies-arrayexpress
TranscriptomicsTranscription profiling by array of Clostridium acetobutylicum grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms.
Clostridium acetobutylicum was grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms. mRNA was extracted, amplified and used on Combimatrix custom arrays to obtain an expression profile. Analysis was perf...
ORGANISM(S): Clostridium acetobutylicum 
2010-07-09 | E-MTAB-267 | biostudies-arrayexpress
TranscriptomicsRat Semi-Circular Canal Duct Gene Expression Studies
The goal was to screen for the expressed genes in Semi-Circular Canal Duct (SCCD) that are related to ion transport and its regulation. The objective was to discover which genes changed expression levels in response to glucocorticoids. Keywords: drug response Primary cultures were incubated for 24 h...
ORGANISM(S): Rattus norvegicus 
2010-04-28 | E-GEOD-6197 | biostudies-arrayexpress
TranscriptomicsTranscription profiling by array of Pseudomonas aeruginosa and Enterococcus faecium coculture grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms.
Coculture Pseudomonas aeruginosa and Enterococcus faecium were grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms. mRNA was extracted, amplified and used on Combimatrix custom arrays to obtain an expre...
ORGANISM(S): Pseudomonas aeruginosa 
2010-08-13 | E-MTAB-320 | biostudies-arrayexpress
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