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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 
ProteomicsNative alpha synuclein crosslinking
Alpha synuclein in it's native state in solution was crosslinked using a variety of short-range crosslinking reagents. Crosslinks detected by mass spectrometry were then used as constraints in a discrete molecular dynamics simulation of the synuclein protein, and a structural ensemble of the protein...
ORGANISM(S): Homo sapiens (Human) 
2019-02-28 | PXD011645 | Pride
Alpha synuclein Crosslinking Modelling 
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 
ProteomicsA synthetic crosslinked peptide library for benchmarking crosslinking mass spectrometry search engines
We have created a synthetic crosslinked peptide library to benchmark crosslinking mass spectrometry search engines. The unique benefit of the library is knowing which identified crosslinks are true and which are false. The data collected from mass spectrometry measurements of the peptide library wer...
ORGANISM(S): Streptococcus pyogenes ABC020006030 
2020-07-28 | PXD014337 | Pride
Crosslinking mass spectrometry peptide library 
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 
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 
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 
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 
GenomicsHydrogel crosslinking modulates macrophages, fibroblasts, and their communication, during wound healing
Hydrogel crosslinking modulates macrophages, fibroblasts, and their communication, during wound healing
PRJNA1044423 | ENA
GenomicsIdentifying METTL5-bound RNA by crosslinking-assisted immunoprecipitation
Identifying METTL5-bound RNA by crosslinking-assisted immunoprecipitation
PRJNA729821 | ENA
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