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ProteomicsIn vitro crosslinking of PAX8 and PRDM3
MS crosslinking of PAX8 and PRDM3 using standard DSSO-based crosslinking
ORGANISM(S): Homo sapiens (Human) 
2021-03-09 | PXD021708 | Pride
Prdm3 Xlinkx Crosslinking-ms Pax8 
ProteomicsDeciphering Photosynthetic Protein Networks: A Crosslinking-MS Strategy for Studying Functional Thylakoid Membranes
Photosynthesis relies on a dynamic network of protein-protein interactions that adapt to fluctuating light conditions. We present an XL-MS pipeline applied directly to functional thylakoid membranes from Arabidopsis thaliana and Spinacia oleracea. By combining PhoX crosslinker with the amphiphilic s...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) Spinacia sp. 
2026-05-14 | PXD068425 | Pride
Arabidopsis thaliana Crosslinking-ms Thylakoid membranes Photosynthesis Protein-protein interactions Structural proteomics Spinacia oleracea 
ProteomicsCrosslinking MS to elucidate the Architecture of the Nucleosome Remodelling and Deacetylase (NuRD) complex
The Nucleosome Remodeling and Deacetylase (NuRD) complex is essential for development in complex animals but has been refractory to detailed analysis because of its low abundance and resistance to recombinant production. In combination with other techniques, crosslinking mass spectrometry was used t...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) 
2021-01-08 | PXD010111 | Pride
Crosslinking ms Structural proteomics Nurd 
ProteomicsLarge-scale qualitative and quantitative research of dityrosine crosslinking omics in Escherichia coli
Excessive reactive oxygen species cause oxidative stress in cells. Two molecules of tyrosine can generate dityrosine, which is not only a product of natural posttranslational processes, but also a putative biomarker for protein oxidation. Few studies have investigated dityrosine crosslinking under e...
ORGANISM(S): Escherichia coli 
2023-05-10 | PXD039132 | Pride
Hydrogen peroxide Dityrosine crosslinking Label-free proteomics 
MetabolomicsMetabolomics profiling (GC-MS and LC-MS) for time-course differentiation of pre-B cells-like (B3 cell line) under the controlled induction of the transcription factor Ikaros (STATegra Project)
The main goal of the project is to develop a new generation of bioinformatics resources for the integrative analysis of multiple types of 'omics data. These resources include both novel statistical methodologies as well as user-friendly software implementations. STATegra methods address many aspects...
2016-12-15 | MTBLS283 | MetaboLights
ProteomicsHistone interaction landscapes visualized by crosslinking mass spectrometry in intact cell nuclei
Cells organize their actions partly through tightly controlled protein-protein interactions – collectively termed the interactome. Here we use crosslinking mass spectrometry (XL-MS) to chart the interactome of intact human nuclei. We overall identified ~8700 crosslinks, of which 2/3 represent links ...
ORGANISM(S): Homo sapiens (Human) 
2018-07-23 | PXD007513 | Pride
Crosslinking mass spectrometry Histone interaction network – ptm interplay Nuclear interactome Histone variant specific interactions Nuclear protein-protein interactions 
ProteomicsClick-linking: a cell-compatible protein crosslinking method based on click chemistry
We developed a novel approach to in situ crosslinking mass spectrometry (XL-MS) where the reaction is split into two sequential and orthogonal coupling events. The method involves pre-stabilization of the proteome using a fixation protocol, followed by a two-step process that begins with extensive l...
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2025-01-28 | PXD059118 | Pride
In situ Crosslinking Proteome-wide Protein-protein interactions Interactome 
ProteomicsGlobal Membrane Protein Interactome Analysis using In vivo Crosslinking and MS-based Protein Correlation Profiling
We present a methodology using in vivo crosslinking combined with HPLC-MS for the global analysis of endogenous protein complexes by protein correlation profiling. Formaldehyde crosslinked protein complexes were extracted with high yield using denaturing buffers that maintained complex solubility du...
ORGANISM(S): Homo sapiens (Human) 
2016-04-27 | PXD003754 | Pride
Proteomics  protein complexes  protein crosslinking  mass spectrometry Membrane protein  interactome analysis 
ProteomicsIntegrative Threading of the DNA-PKcs Disordered Region with Crosslinking Restraints
Integrative structure modelling was applied to understand how auto-phosphorylation of the ABCDE cluster in DNA-PKcs can occur. We used crosslinking restraints to assign sequence to structurally unassigned helices in DNA-PKcs s in the largely disordered region containing the ABCDE cluster. Our final ...
ORGANISM(S): Homo sapiens (Human) 
2019-12-10 | PXD016639 | Pride
Crosslinking-ms Integrative modelling Dna-pkcs 
ProteomicsGlobal Membrane Protein Interactome Analysis using In vivo Crosslinking and MS-based Protein Correlation Profiling
We present a methodology using in vivo crosslinking combined with HPLC-MS for the global analysis of endogenous protein complexes by protein correlation profiling. Formaldehyde crosslinked protein complexes were extracted with high yield using denaturing buffers that maintained complex solubility du...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2016-08-02 | MSV000080014 | MassIVE
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