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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 
ProteomicseXL-MS: An enhanced Cross-Linking Mass Spectrometry Workflow to Study Protein Complexes.
The analysis of proteins and protein complexes by cross-linking mass spectrometry (XL-MS) has expanded in the last dec-ade. However, mostly used approaches suffer important limitations in term of efficiency and sensitivity. We describe here a new workflow based on the advanced use of the trifunction...
ORGANISM(S): Oryctolagus cuniculus (Rabbit) 
2021-08-11 | PXD010422 | Pride
Creatine kinase Mass spectrometry Cross-link Monoavidin biotin affinty enrichment Click chemistry 
ProteomicsCross-linking MS supporting: Structural stabilization of the intrinsically disordered SARS-CoV-2 N by binding to RNA sequences engineered from the viral genome
The nucleocapsid N is one of four structural proteins of the coronaviruses. Its essential role in genome encapsidation makes it a critical therapeutic target for COVID-19 and related diseases. However, the inherent disorder of full-length N has hampered its structural analysis. Here, we describe a s...
ORGANISM(S): Severe acute respiratory syndrome coronavirus 2 
2025-07-21 | PXD052584 | Pride
Cross-linking Xl-ms Sars-cov-2 n 
ProteomicsIn vivo cross-linking supports a head-to-tail mechanism for regulation of the plant plasma membrane P-type H+-ATPase
In higher plants, a P-type proton pumping ATPase generates the proton-motive force essential for the function of all other transporters and for proper growth and development. X-ray crystallographic studies of the plant plasma membrane proton pump have provided information on amino acids involved in...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2018-09-24 | PXD010892 | Pride
And arabidopsis thaliana Mass spectrometry Protein cross-linking Protein-protein interaction H+-atpase 
ProteomicsDeveloping In Vivo Cross-linking Mass Spectrometry (XL-MS) to Decipher Protein Interaction Landscapes at the Proteome Scale
We have developed a new and robust in vivo cross-linking mass spectrometry (XL-MS) that utilizes a multifunctional MS-cleavable cross-linker to enable the efficient capture, enrichment, and identification of in vivo cross-linked peptides at the whole proteome scale.
ORGANISM(S): Homo sapiens (Human) 
2021-07-30 | PXD012788 | Pride
Human Lc-ms Cross-linking mass spec Ms-cleavable Click chemistry Enrichable Proteome wide 
ProteomicsNuclei cross-linking mass spectrometry
Cross-linking mass spectrometry performed on intact nuclei purified from HEK293T for structural interactome profiling of the nuclear pore complex
ORGANISM(S): Homo sapiens (Human) 
2026-09-21 | PXD080872 | Pride
Human Nuclear pore complexes 
ProteomicsStructural Assessment of the Full-Length Tumor Suppressor Protein p53 by Mass Spectrometry-Guided Computational Modeling
The tetrameric tumor suppressor p53 represents a great challenge for 3D structural analysis due to its high degree of intrinsic disorder (ca. 40%). We developed and applied an integrative structural biology approach combining complementary techniques of structural mass spectrometry (MS), namely cros...
ORGANISM(S): Escherichia coli 
2023-06-26 | PXD037030 | Pride
Computational modeling  cross-linking mass spectrometry  dna binding  intrinsically disordered proteins  tumor suppressor p53 
ProteomicsSignal Attrition in Whole Cell Crosslinking Mass Spectrometry
We investigated points in the typical sample workflow that could contribute to the perceived low cross-linking yields. We demonstrate, through a 2-step cross-linking strategy called Click-Linking, that the chemical reaction is not the main contributor to the low number of identified cross-links. We ...
ORGANISM(S): Homo sapiens (Human) 
2025-11-18 | PXD069512 | Pride
Cross-linking Xl-ms Reaction yield 
ProteomicsImproving identification of in-organello protein-protein interactions using an affinity-enrichable, isotopically-coded, and mass spectrometry-cleavable chemical crosslinker
An experimental and computational approach for identification of protein-protein interactions by in-vivo chemical crosslinking and mass spectrometry (CLMS) has been developed that takes advantage of the specific characteristics of cyanurbiotindipropionylsuccinimide (CBDPS), an affinity-tagged isotop...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2020-03-17 | PXD014055 | Pride
Cross-linking Yeast Mitochondria 
ProteomicsImproving identification of in-organello protein-protein interactions using an affinity-enrichable, isotopically-coded, and mass spectrometry-cleavable chemical crosslinker
An experimental and computational approach for identification of protein-protein interactions by in-vivo chemical crosslinking and mass spectrometry (CLMS) has been developed that takes advantage of the specific characteristics of cyanurbiotindipropionylsuccinimide (CBDPS), an affinity-tagged isotop...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2020-03-17 | PXD017066 | Pride
Cross-linking Yeast Mitochondria 
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