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MetabolomicsProtein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase

Metabolic networks are interconnected and influence diverse cellular processes. The protein-metabolite interactions that mediate these networks are frequently low affinity and challenging to systematically discover. We developed mass spectrometry integrated with equilibrium dialysis for the disco...

2023-08-07 | MTBLS7237 | MetaboLights
MetabolomicsEvidence for quorum sensing and differential metabolite production by Ruegeria pomeroyi in response to DMSP
Microbial alteration and remineralization of organic matter in the ocean play essential roles in the carbon cycle. The impact of individual compounds as either growth substrates or infochemicals is still poorly constrained in models, particularly for organisms with relatively versatile genomes. Here...
2015-01-29 | MTBLS157 | MetaboLights
MetabolomicsDifferential interactions of dietary EPA and DHA with the gut microbiota dictate distinct metabolic outcomes in the host

Background: Docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) are known to modulate host physiology, but their differential interactions with the gut microbiota and consequent host metabolic effects remain poorly understood.

Methods: We employed shotgun metagenomics, untargeted met...

2026-01-31 | MTBLS13495 | MetaboLights
MetabolomicsDifferential interactions of dietary EPA and DHA with the gut microbiota dictate distinct metabolic outcomes in the host

Background: Docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) are known to modulate host physiology, but their differential interactions with the gut microbiota and consequent host metabolic effects remain poorly understood.

Methods: We employed shotgun metagenomics, untargeted met...

2026-01-31 | MTBLS13497 | MetaboLights
TranscriptomicsRNA-Seq profiling of single bovine oocyte transcript abundance and its modulation by cytoplasmic polyadenylation
Polyadenylated RNA from individual germinal vesicle and metaphase II ooyctes was amplified and processed for Illumina sequencing. Increases in polyadenylated transcript abundance were observed and are likely due to cytoplasmic polyadenylation. Transcriptomic analysis of GV and MII bovine oocytes.
ORGANISM(S): Bos taurus 
2015-07-08 | E-GEOD-61717 | biostudies-arrayexpress
TranscriptomicsComparison of relative transcript and protein abundance in Plasmodium falciparum schizont stage parasites
Background: Malaria is a one of the most important infectious diseases and is caused by parasitic protozoa of the genus Plasmodium. Previously, the quantitative characterization of the P. falciparum transcriptome demonstrated that the strictly controlled progression of these parasites through their ...
ORGANISM(S): Plasmodium falciparum 
2010-05-05 | E-GEOD-13251 | biostudies-arrayexpress
ProteomicsProtein abundance of AKT and ERK pathway components governs cell-type-specific regulation of proliferation
Signaling through the AKT and ERK pathways controls cell proliferation. However, the integrated regulation of this multistep process, involving signal processing, cell growth and cell-cycle progression, is poorly understood. Here we study different murine hematopoietic cell types, in which AKT and E...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-31 | MSV000080844 | MassIVE
Proteomicsmsqrob2PTM: differential abundance and differential usage analysis of MS-based proteomics data at the post-translational modification and peptidoform level
In the era of open-modification search engines, more post-translational modifications than ever can be detected by LC-MS/MS-based proteomics. This development can switch proteomics research into a higher gear, as PTMs are key in many cellular pathways important in cell proliferation, migration, meta...
ORGANISM(S): Homo sapiens (Human) 
2024-06-16 | PXD043476 | Pride
Msqrob2ptm Ptm Msqrob Peptidoform 
ProteomicsDEqMS - a method for differential protein expression analysis of quantitative mass spectrometry data
DEqMS is a statistical method to perform differential protein expression (abundance) analysis for quantitative mass spectrometry-based proteomics. Developed on top of Limma, DEqMS implements a robust Bayesian method for accurate variance estimation while taking into account the number of peptide pre...
ORGANISM(S): Homo sapiens (Human) 
2026-06-03 | PXD063099 | Pride
Differential abundance Dia Label-free proteomics Statistical method Differential expression Lc-ms/ms 
TranscriptomicsAbsolute quantification of protein production reveals principles underlying protein synthesis rates
A quantitative view of cellular functions requires precise measures of the rates of biomolecule production, especially proteins-the direct effectors of biological processes. Here we present a genome-wide approach, based on ribosome profiling, for measuring absolute protein synthesis rates. The resul...
ORGANISM(S): Escherichia coli 
2014-04-24 | E-GEOD-53767 | biostudies-arrayexpress
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