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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 
Proteomics"In-gel cross-linking mass spectrometry (IGX-MS) of proteins and protein complexes"
Cross-linking mass spectrometry has developed into an important method to study protein structures and interactions. The in-solution cross-linking workflows involve time and sample consuming steps and do not provide sensible solutions for differentiating cross-links obtained from co-occurring protei...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) Escherichia coli 
2020-12-14 | PXD020014 | Pride
Bn-page/ cross-linking/ protein complexes/ complement/ protein modeling 
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 
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 
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 
ProteomicsAn Amphibious Bi-functional Probe For Protein Chemical Cross-linking.
Chemical cross-linking mass spectrometry (CXMS) has emerged as a powerful and well-established method for probing protein structure, conformational dynamics, and protein–protein interactions, particularly in cases where classical high-resolution techniques face intrinsic limitations. The development...
ORGANISM(S): Homo sapiens (Human) Equus caballus (Horse) 
2026-07-13 | PXD074784 | Pride
Togni reagents Radical labeling Chemical cross-linking Mass spectrometry Protein footprinting Fluoroalkylation : protein structure 
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 
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 
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 
ProteomicsSingle Nucleotide Resolution RNA-Protein Cross-Linking/MS: Simple Extension of the CLIR-MS Workflow
RNA-protein interactions mediate a vast number of intracellular processes. CLIR-MS (cross-linking of isotope labeled RNA and tandem mass spectrometry) is a mass spectrometric technique that allows the identification of RNA-protein interaction sites at single nucleotide/amino acid resolution in a sin...
ORGANISM(S): Homo sapiens (Human) 
2021-11-04 | PXD024010 | Pride
Protein rna cross-linking clir-ms uv xl 
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