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MetabolomicsSpatial metabolomics of in situ, host-microbe interactions (MALDI imaging MS assay)
Spatial metabolomics describes the location and chemistry of small molecules involved in metabolic phenotypes, defense molecules and chemical interactions in natural communities. Most current techniques are unable to spatially link the genotype and metabolic phenotype of microorganisms in situ at a ...
2019-11-15 | MTBLS744 | MetaboLights
MetabolomicsSpatial metabolomics of in situ, host-microbe interactions (On-tissue MALDI imaging MS/MS assay)
Spatial metabolomics describes the location and chemistry of small molecules involved in metabolic phenotypes, defense molecules and chemical interactions in natural communities. Most current techniques are unable to spatially link the genotype and metabolic phenotype of microorganisms in situ at a ...
2019-11-15 | MTBLS805 | MetaboLights
ProteomicsOptimized cross-linking mass spectrometry for in situ interaction proteomics
ecent development of mass spectrometer cleavable protein cross-linkers and algorithms for their spectral identification now permits large-scale cross-linking mass spectrometry (XL-MS). Here, we optimized the use of cleavable disuccinimidyl sulfoxide (DSSO) cross-linker for labeling native protein co...
ORGANISM(S): Homo sapiens (Human) 
2019-04-03 | PXD010796 | Pride
Human Cross-linking mass spectrometry Chromatin 
ProteomicsTargeted in situ cross-linking for determination of structure and interactions of SARS-CoV-2 proteins in the cellular context
Cross-linking mass spectrometry (XL-MS) has progressed from studying purified protein assemblies in-vitro towards investigating the same assemblies in intact cells, tissues, and even whole organisms (so called “in situ XL-MS”). In situ XL-MS offers the great advantage of reporting on the architectur...
ORGANISM(S): Homo sapiens (Human) 
2021-10-06 | PXD023487 | Pride
Mass-spectrometry Xlms Sars-cov-2 Clms Hek293 Nucleocapsid protein Lc-msms Nsp1 Nsp2 
ProteomicsChemical cross-linking enables drafting ClpXP proximity maps and taking snapshots of in vivo interaction networks
Protein-protein interactions within complexes and networks are often dynamic and their elucidation remains a challenging task. Here, we show on the example of the proteolytic ClpXP complex the power of combined chemical cross-linking and mass-spectrometry to capture transient binding interactions wi...
ORGANISM(S): Homo sapiens (Human) Escherichia coli Staphylococcus aureus 
2018-11-21 | PXD009224 | Pride
Clpxp Interacting proteins Chemical cross-linking Co-ip Clpp 
ProteomicsFacilitating in situ cross-linking and mass spectrometry by antibody-based protein enrichment
Cross-linking of living cells followed by mass spectrometry identification of cross-linked peptides (in situ CLMS) is an emerging technology to study protein structures in their native environment. One of the inherent difficulties of this approach is the high complexity of the samples following cell...
ORGANISM(S): Homo sapiens (Human) 
2022-06-09 | PXD025099 | Pride
Cl-ms Antibody 
Proteomics3D topology of the SMC2/SMC4 sub-complex from chicken condensin I revealed by cross-linking and molecular modelling
SMC proteins are essential components of three protein complexes that are important for chromosome structure and function. The cohesin complex holds replicated sister chromatids together, whereas the condensin complex has an essential role in mitotic chromosome architecture. Both are involved in int...
ORGANISM(S): Gallus gallus (Chicken) 
2015-07-13 | PXD001835 | Pride
Condensin Cross-linking Mass spectrometry Smc Structure Coiled-coil 
ProteomicsMass spectrometry study of formaldehyde cross-linking of structured proteins
Formaldehyde is a widely used fixative in biology and medicine. The current chemical model for formaldehyde cross-linking of proteins is the formation of a methylene bridge that incorporates one carbon atom into the link. Here, we present mass spectrometry data that largely refute this model. Instea...
ORGANISM(S): Homo sapiens (Human) 
2020-06-25 | PXD015435 | Pride
Xl-ms Nascent polypeptide-associated complex Actin Structural biology Cross-linking coupled to mass spectrometry 
ProteomicsTargeted cross-linker delivery for in situ mapping of protein conformations and interactions in mitochondria
Current methods for intracellular protein analysis mostly require the separation of specific organelles or the change of intracellular environment. However, the functions of these proteins are determined by their native microenvironment as they usually form complexes with ions, nucleic acids, and ot...
ORGANISM(S): Homo sapiens (Human) 
2023-05-26 | PXD035433 | Pride
Mitochondria In-situ cross-linking Nanoparticles delivery Protein conformations and interactions Chemical cross-linking mass spectrometry 
TranscriptomicsSpatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization
Though important for gene regulation most studies of genome organisation use either fluorescence in situ hybridisation (FISH) or chromosome conformation capture (3C) methods. FISH directly visualises the spatial relationship of sequences, but is usually applied to a few loci at a time. The frequency...
ORGANISM(S): Mus musculus 
2015-01-02 | E-GEOD-61814 | biostudies-arrayexpress
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