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ProteomicsLight-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks
Delineating the extracellular interaction network of the cell surface proteotype (the surfaceome) is fundamental to understanding cellular signaling function in health and disease. Here, we developed LUX-MS, an optoproteomic technology that enables the spatiotemporal and proteome-wide study of surfa...
ORGANISM(S): Mus musculus (Mouse) Homo sapiens (Human) Listeria monocytogenes serotype 4b Listeria phage A500 Escherichia coli 
2021-06-14 | PXD020481 | Pride
Lc-ms/ms 
UnknownHyperbolic mapping of human proximity networks.
Not available
S-EPMC7679465 | biostudies-literature
ProteomicsHepatic palmitoyl-proteomes and acyl-protein thioesterase protein proximity networks link lipid modification and mitochondria
Elevated fatty acids are associated with insulin resistance. Fatty acids can reversibly modify proteins through a process known as S-palmitoylation. To test the hypothesis that depalmitoylation by acyl-protein thioesterases 1 and 2 (APT1 and APT2) in the liver regulates glucose metabolism, we genera...
ORGANISM(S): Mus musculus (Mouse) 
2023-11-05 | PXD041552 | Pride
Lipid Proteomics Palmitoylation Mitochondria Proximity networks 
UnknownProximity Graph Networks: Predicting Ligand Affinity with Message Passing Neural Networks.
Not available
S-EPMC11267574 | biostudies-literature
UnknownHow Physical Proximity Shapes Complex Social Networks.
Not available
S-EPMC6286340 | biostudies-literature
ProteomicsTime-resolved proximity labeling of protein networks associated with ligand-activated EGFR
Ligand binding to the EGF receptor (EGFR) initiates signal transduction and endocytosis of the receptor. The mechanisms of endocytosis and regulation of signaling by endocytosis are poorly understood. Here, we combined peroxidase-catalyzed proximity labeling, isobaric peptide tagging and quantitativ...
ORGANISM(S): Homo sapiens (Human) 
2022-06-04 | PXD030072 | Pride
Proteomics analysis Tmt Endocytosis Tfg Egfr Proximity labeling 
ProteomicsA method for spatially and temporally resolved protein network interrogation in living cells
Cells operate through protein interaction networks organized in space and in time, but current methods to interrogate such biology typically resolve only one of these dimensions. Here, we describe a method to resolve both dimensions simultaneously using proximity labeling mediated by engineered asco...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2020-01-29 | MSV000084857 | MassIVE
ProteomicsArabidopsis thaliana ASK1 proximity labeling upon Pst DC3000 infection
we used proximity labeling of ASK1, a core SCF adaptor, to profile dynamic changes in SCF-associated networks during Pseudomonas syringae infection. This analysis revealed widespread remodeling of F-box proteins and immune-related regulators, including several previously uncharacterized components.
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2026-03-05 | PXD063820 | Pride
Skp1 Turboid Ask1 Proteasome Proximity labelling Arabidopsis 
ProteomicsProximity-dependent biotinylation by TurboID to identify protein-protein interaction networks in yeast
The use of proximity-dependent biotinylation assays coupled to mass spectrometry (PDB-MS) has changed the field of protein-protein interactions (PPI) studies. Yet, despite the recurrent and successful use of BioID-based PPI screening in mammalian cells, the implementation of PDB-MS in yeast has not ...
ORGANISM(S): Schizosaccharomyces pombe 927 
2019-05-16 | PXD013183 | Pride
Proximity-dependent biotinylation  turboid  yeast  s. pombe  rmt3 Rna exosome 
ProteomicsAn Approach to Spatiotemporally Resolve Protein Interaction Networks in Living Cells - B2AR_localization
SRM assays were generated for selected interactors of B2AR and DOR (MSV000084857), as well as for localization controls and ribosomal proteins (RPL18A, RPL28, RPL3, RPL35A, RPL6) as internal controls for normalization (Table S5 in publication). We selected localization markers for different cellular...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2020-02-17 | MSV000084967 | MassIVE
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