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MetabolomicsIntegrating two chromatographies in a co-fractionation mass spectrometry approach improved protein-metabolite interactions (PMIs) mapping capabilities and revealed novel protein-ligand pairings in Escherichia coli.
The protein-metabolite interactome remains understudied. We previously developed a co-fractionation mass-spectrometry-based approach called PROMIS to address this gap. PROMIS relies on size separation chromatography of protein-metabolite complexes from lysates, followed by proteomics and metabolomic...
2025-04-25 | MTBLS9098 | MetaboLights
MetabolomicsNatural photosynthetic system for restoring homeostasis of animal organelle interaction network

Disruption of organelle interactions due to metabolic stress is a crucial factor in the pathological processes of many degenerative diseases. Current treatments usually focus on individual organelles while ignoring the role of organelle interactions in cell damage caused by cascade reactions. The...

2026-01-20 | MTBLS13730 | MetaboLights
MetabolomicsDisturbed Microbiota-Metabolites-Immune Interaction Network is Associated with Olfactory Dysfunction in Patients with Chronic Rhinosinusitis

PURPOSE: Olfactory dysfunction (OD) is a debilitating symptom frequently reported by patients with chronic rhinosinusitis (CRS) and it is associated with a dysregulated sinonasal inflammation. However, little information is available about the effect of the inflammation-related n...

2023-05-12 | MTBLS7584 | MetaboLights
MetabolomicsMulti-level analysis of gut microbiome extracellular vesicles-host interaction reveals a connection to gut-brain axis signaling.

Microbiota-released extracellular vesicles (MEVs) have emerged as a key player in intercellular signaling. However, their involvement in the gut-brain axis has been poorly investigated. In this study, we aimed to investigate the cargo capacity of MEVs for bioactive metabolites and their interacti...

2025-08-12 | MTBLS8494 | MetaboLights
ProteomicsA Detergent-Free Grinding Sample Preparation Method Dramatically Enhances PELSA for Mapping Integral Membrane Protein-Ligand Interaction
The conventional use of detergent-containing buffers for integral membrane protein (IMP) extraction may disrupt native protein conformations, potentially compromising the performance of ligand target identification. As a result, there is a lack of reliable, unbiased, detergent-free proteomic method...
ORGANISM(S): Homo sapiens (Human) 
2025-10-15 | PXD064146 | Pride
Sample preparation  membrane protein  protein-ligand interaction 
ProteomicsLigand-dependent spatiotemporal signaling profiles of the mu-opioid receptor are controlled by distinct protein-protein interaction networks
Ligand-dependent differences in the regulation and internalization of the mu-opioid receptor (MOR) have been linked to the degree of severity of the side effects that limit the use of opiates in the treatment of pain. For example, activation of the MOR by morphine and DAMGO ([D-Ala2,N-MePhe4,Gly-ol]...
ORGANISM(S): Homo sapiens (Human) 
2019-09-26 | PXD013328 | Pride
Proteomics Ras‐related c3 botulinum toxin substrate 1 (rac1) Extracellular signal regulated kinase (erk) Desmosome G protein-coupled receptor (gpcr) Cell compartmentalization Protein complex Opioid 
ProteomicsHigH-ratiO partiaL proteolysiS with carriER proteome (HOLSER) Enables Global Structure Profiling and Site-resolved Elucidation of Ligand-Protein Interactions
Understanding how cellular proteins interact with their environment, including endogenous and exogeneous molecules, is critical for elucidating mechanisms of cellular regulation and drug action. Partial proteolysis-based techniques offer peptide-level resolution of ligand-induced conformational chan...
ORGANISM(S): Homo sapiens (Human) 
2026-09-14 | PXD077592 | Pride
Proteomics Ligand-protein interaction Partial proteolysis Lc-ms-ms 
TranscriptomicsTranscription profiling of mouse spermatagonia stimulated with kit ligand, bone morphogenetic protein 4 (BMP4) or all-trans retinoic acid
wide genome analysis of difference in gene expression induced by treatment with kit ligand (KL), or bone mprphogenetic protein 4 (BMP4), or all-trans retinoic acid in spermatogonia from 7-day-old mice, using Mouse Genome 430 2.0 Array from Affymetrix, representing approximately 45000 mouse known gen...
ORGANISM(S): Mus musculus 
2007-08-01 | E-MEXP-1126 | biostudies-arrayexpress
MetabolomicsPROMIS, global analysis of PROtein-Metabolite Interactions using Size separation in Arabidopsis thaliana
Small molecules not only represent cellular building blocks and metabolic intermediates, but also regulatory ligands and signaling molecules that interact with proteins. Although these interactions affect cellular metabolism, growth, and development, they have been largely understudied. Herein, we d...
2018-07-19 | MTBLS94 | MetaboLights
ProteomicsSILAC-Based Strategy for Proteome-Wide Analysis of Protein-Ligand Binding Interactions (Part 2/2)
A quantitative mass spectrometry-based proteomics method for the large-scale thermodynamic analysis of protein-ligand binding interactions. The methodology utilizes a chemical modification strategy termed, Stability of Proteins from Rates of Oxidation (SPROX), in combination with a Stable Isotope L...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2014-07-31 | PXD000860 | Pride
Shot-gun proteomics Yeast Cyclosporine a Atp 
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