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ProteomicsCrosslinking-Mass Spectrometry data for structural analysis of Doublecortin-Microtubule interaction
Doublecortin (DCX) is a microtubule (MT) associated protein that regulates MT structure and function during neuronal development and mutations in DCX lead to a spectrum of neurological disorders. The structural properties of MT-bound DCX remain poorly resolved. Here, we describe the molecular archit...
ORGANISM(S): Homo sapiens (Human) Sus scrofa domesticus (domestic pig) 
2022-05-04 | PXD033167 | Pride
Crosslinking-mass spectrometry Doublecortin Integrative structural modeling Microtubule 
ProteomicstRNA binding to KEOPS human protein complex
N6-theronylcarbomyl adenosine (t6A) is a universal tRNA posttranscriptional modification that promotes translation fidelity and is therefore required for the fitness of virtually all living cells. Kae1, the t6A modifying enzyme in eukaryotes and archea, resides within the KEOPS complex with three au...
ORGANISM(S): Homo sapiens (Human) 
2020-12-11 | PXD018007 | Pride
Trna Keops Hx-ms 
ProteomicsIntegrative Structural Model of DNA-PK Synapsis
In non-homologous end joining repair of DNA double strand breaks, DNA dependent protein kinase catalytic subunit (DNA-PKcs) and Ku70/80 binds the free DNA ends forming the holoenzyme DNA-PK. DNA-PK synapses across the break to tether the broken ends in the initial long range synaptic complex. We gen...
ORGANISM(S): Homo sapiens (Human) 
2021-01-20 | PXD017931 | Pride
Dna-pk Hydrogen deuterium exchange Crosslinking 
ProteomicsIMProv: A Resource for Crosslink-Driven Structure Modeling that Accommodates Protein Dynamics
Crosslinking and hydrogren-deuterium exchange data of Polycomb Repressive Complex 2 used for integrative modelling.
ORGANISM(S): Homo sapiens (Human) 
2021-10-12 | PXD022861 | Pride
Crosslinking mass spectrometry Software Integrative modelling 
ProteomicsKinetic Analysis of DNA Dependent Protein Kinase Catalytic Subunit
We investigated the dynamics of protein kinase DNA dependent protein kinase catalytic subunit (DNA-PKcs) through hydrogen deuterium exchange mass spectrometry. Over 1100 peptides could be monitored throughout the kinetics experiment, showing the utility of our nanospray HX-MS configuration for ultr...
ORGANISM(S): Homo sapiens (Human) 
2019-12-10 | PXD016595 | Pride
Hdx-ms Nanospray hx-ms Human Dna-pkcs 
ProteomicsConventional cell fixation improves performance of in situ crosslinking mass spectrometry while preserving cellular ultrastructure
We developed an approach to in situ XL-MS which utilizes pre-stabilization with formaldehyde prior to crosslinker introduction. Applications of this method can boost crosslinker signal and allows for membrane-impermeable reagents to be used for studying protein-interaction landscapes in intact human...
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2024-04-12 | PXD051075 | Pride
In situ xl-ms Formaldehyde fixaiton Crosslinking mass spectrometry 
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 
ProteomicsImproving spectral validation rates in hydrogen-deuterium exchange data analysis.
HX-MS data generated to support the testing and development of the HX data analysis applications in Mass Spec Studio.
ORGANISM(S): Homo sapiens (Human) Oryctolagus cuniculus (Rabbit) 
2021-02-22 | PXD022831 | Pride
Hx-deal Hdx-ms Mass-spec studio Proteasome Hx-pipe Eg5 
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 
ProteomicsAutomating data analysis for hydrogen/deuterium exchange mass spectrometry using data-independent acquisition methodology
We developed an HX-MS2 strategy that supports the acquisition of CID-generated fragment ions alongside their peptide precursors. The approach enables true auto-validation of HX data by mining the rich set of deuterated fragments, using the extra dimension of data to simultaneously confirm the peptid...
ORGANISM(S): Homo sapiens (Human) Oryctolagus cuniculus (Rabbit) 
2023-09-08 | PXD045012 | Pride
Dia Lc-ms Swath-ms Dna-pk Hx-ms 
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