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ProteomicsOn the reproducibility of label-free quantitative cross-linking/mass spectrometry
Quantitative cross-linking/mass spectrometry (QCLMS) is an emerging approach to study conformational changes of proteins and multi-subunit complexes. Distinguishing protein conformations requires reproducibly identifying and quantifying cross-linked peptides. Here we analyzed the variation between m...
ORGANISM(S): Homo sapiens (Human) 
2018-01-02 | PXD007250 | Pride
Cross-linking Mass-spectrometry Skyline Quatitation 
ProteomicsA Simple Cross-Linking/Mass Spectrometry Workflow to Study System-Wide Protein Interactions in Drosophila Embryos
We provide a cross-linking/MS workflow that can be applied to complex systems. The software tool MeroX 2.0 can be used to identify cross-linked peptide on a proteome-wide level. We applied the workflow to extracts of Drosophila embryos and identified 5,129 unique cross-linked residue pairs in biolog...
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2019-07-09 | PXD012546 | Pride
Cross-linking Mass spectrometry Xlms Cxms Drosophila 
ProteomicsQuantitative cross-linking/mass spectrometry
Dynamic proteins and multi-protein complexes govern most biological processes. Cross-linking/mass spectrometry (CLMS) is increasingly successful in providing residue- resolution data on static proteinaceous structures. Here we investigate the technical feasibility of recording dynamic processes usin...
ORGANISM(S): Homo sapiens (Human) 
2015-06-08 | PXD002142 | Pride
Protein dynamics Structual biology Quantitation Cross-linking 
ProteomicsIdentification of human PKD2 interaction partners from cytosolic protein fractions of HeLa cells by affinity enrichment cross-linking/MS
We investigated the interaction network of human PKD2 in the cytosol as well as in Golgi-enriched subcellular protein fractions, using an affinity enrichment strategy combined with chemical cross-linking/mass spectrometry (MS). Analysis of the subproteomes revealed the presence of distinct proteins ...
ORGANISM(S): Homo sapiens (Human) 
2016-09-27 | PXD003909 | Pride
Human Pkd2 Cross-linking/ms Affinity enrichment Orbitrap fusion 
ProteomicsStructural requirements for photo-induced RNA-protein cross-linking
Cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) was used to study the UV cross-linking behavior of in vitro reconstituted FOX1 RRM in complex with its cognate RNA sequence, the Fox binding element (FBE), (U)GCAUGU. The FBE heptanucleotide was subsequently mutated, and ...
ORGANISM(S): Homo sapiens (Human) 
2022-06-09 | PXD031381 | Pride
Uv cross-linking  mbnl1  fox1  ptbp1  sf3a1  u1  u2  cross-linking  xl-ms  structural proteomics  protein-rna  rna-protein  protein-rna complex  rna-protein complex  clir-ms 
ProteomicsIdentification of human PKD2 interaction partners from Golgi-enriched protein fractions of HeLa cells by affinity enrichment cross-linking/MS
We investigated the interaction network of human PKD2 in the cytosol as well as in Golgi-enriched subcellular protein fractions, using an affinity enrichment strategy combined with chemical cross-linking/mass spectrometry (MS). Analysis of the subproteomes revealed the presence of distinct proteins ...
ORGANISM(S): Homo sapiens (Human) 
2016-09-27 | PXD003913 | Pride
Human Pkd2 Hela cells Cross-linking/ms Affinity enrichment Golgi apparatus Orbitrap fusion 
ProteomicsAnalysis of bilirubin-induced bovine serum albumin stability using protein denaturation and quantitative cross-linking mass spectrometry
We report the combination of protein-denaturation stability principles with quantitative cross-linking mass spectrometry using isobaric quantitative protein interaction reporter technologies. This method enables the evaluation of ligand-induced protein engagement through analysis of cross-link rela...
ORGANISM(S): Bos taurus (Bovine) 
2024-07-03 | PXD036649 | Pride
Quantitative cross-linking Protein stability Mass spectrometry 
ProteomicsCharacterizing the dynamic oligomerization of Hsp90β using photo-cross-linking
Cross-linking mass spectrometry (XL-MS) is a powerful tool for probing protein structures. While conventional chemical cross-linkers react with specific residues with defined chemistry, photo-cross-linkers, despite their superior reactivity, have been hindered by incomplete mechanistic understanding...
ORGANISM(S): Homo sapiens (Human) 
2026-04-09 | PXD072009 | Pride
Hsp90 Cleavable cross-linkers Diazirine Photo-cross-linking 
ProteomicsA model dataset for quantitative cross-linking/mass spectrometry using isotope-labeled cross-linkers
Dynamic proteins and multi-protein complexes govern most biological processes. Cross-linking/mass spectrometry (CLMS) is increasingly successful in providing residue-resolution data on static proteinaceous structures. In order to investigate the technical feasibility of recording dynamic processes u...
ORGANISM(S): Homo sapiens (Human) 
2016-05-06 | PXD004107 | Pride
Model dataset Isotope-labeled cross-linkers Hsa Quantitative cross-linking/mass spectromentry 
Proteomicscross-linking mass spectrometry of synaptosome
Cross-linking mass spectrometry data of synaptosome and microsome fractions of mouse cerebellum and hippocampus.
ORGANISM(S): Mus musculus (Mouse) 
2020-12-03 | PXD010317 | Pride
Synaptosome Microsome Cross-linking mass spectrometry 
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