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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
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 1/2)
A quantitative mass spectrometry-based proteomics method for the large-scale thermodynamic analysis of protein-ligand binding interactions is described here. The methodology utilizes a chemical modification strategy termed, Stability of Proteins from Rates of Oxidation (SPROX), in combination with ...
ORGANISM(S): Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) 
2014-07-31 | PXD000858 | Pride
Shot-gun proteomics Yeast Cyclosporine a Atp 
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 
MetabolomicsMulti-omic Landscape of Airway Microbe-Host Interactions in Chronic Obstructive Pulmonary Disease

The mechanistic role of the airway microbiome in chronic obstructive pulmonary disease (COPD) remains largely unexplored. We present a landscape of airway microbe-host interactions in COPD by an in-depth profiling of sputum metagenome, metabolome, host transcriptome and proteome from 99 COPD pati...

2022-06-20 | MTBLS4017 | MetaboLights
ProteomicsCarbene Footprinting Accurately Maps Binding Sites in Protein-Ligand and Protein-Protein Interactions
Specific interactions between proteins and their binding partners are fundamental to life processes. Differential protein footprinting using a new and efficient, photo-activated aryltrifluromethylcarbene probe together with mass spectrometry has been employed to identify protein-ligand and protein-p...
ORGANISM(S): Homo sapiens (Human) Gallus gallus (Chicken) 
2016-12-19 | PXD004971 | Pride
Lysozyme Carbene footprinting Usp5 Covalent labelling 
ProteomicsHigh-throughput peptide-centric local stability assay extends protein-ligand identification to membrane proteins, tissues, and bacteria
High-throughput peptide-centric local stability assay extends protein-ligand identification to membrane proteins, tissues, and bacteria
ORGANISM(S): Mus musculus (Mouse) Homo sapiens (Human) Escherichia coli 
2025-09-22 | PXD062869 | Pride
Protein-ligand interactions 
OtherProteomic analysis of the epidermal growth factor receptor (EGFR) interactome and post-translational modifications associated with receptor endocytosis in response to EGF and stress.
Data from ProteomeXchange, PXD ID: PXD000788. File: T1041A_Cont3.mzml. Published as part of Mol Cell Proteomics. 2014 Jul;13(7):1644-58 . From the Abstract: {{i}} ass spectrometry was applied to comprehensively analyze the phosphorylation, ubiquitination, and protein-protein interactions of wild ty...
ORGANISM(S): Homo_sapiens_viruses, Human 
GPM32310004705 | GPMDB
Resource Reanalysis 
ProteomicsMembrane mimetic thermal proteome profiling (MM-TPP) towards mapping membrane protein-ligand dynamic interactions
Integral membrane proteins (IMPs) are key targets for small-molecule therapeutics. However, robust, unbiased, and detergent-free methods to probe on- and off-target interactions within this protein class remain underdeveloped. Previously, we introduced the Peptidisc membrane mimetic (MM) for water-s...
ORGANISM(S): Mus musculus (Mouse) 
2025-11-17 | PXD068828 | Pride
Membrane proteins Orbitrap exploris Mus musculus Membrane mimetic thermal proteome profiling Proteomics 
UnknownStrong Ligand-Protein Interactions Derived from Diffuse Ligand Interactions with Loose Binding Sites.
Not available
S-EPMC4434174 | biostudies-literature
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