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ProteomicsMonolinks Matter: Rational Modification of a Cross-Linker for Improved Flexible Protein Structure Modeling
Chemical cross-linking/mass spectrometry (XL-MS) has emerged as a complementary tool for mapping interaction sites within protein networks as well as gaining moderate-resolution native structurale insight with minimal interference. XL-MS technology mostly relies on chemoselective reactions (crosslin...
ORGANISM(S): Homo sapiens (Human) 
2025-05-06 | PXD051742 | Pride
Protein structure Alphafold Crosslink Dsso-carbamate Monolink 
ProteomicsModeling flexible protein structure with AlphaFold2 and cross-linking mass spectrometry
We propose a pipeline that combines AlphaFold2 (AF2) and crosslinking mass spectrometry (XL-MS) to model the structure of proteins with multiple conformations. The pipeline consists of two main steps: ensemble generation using AF2, and conformer selection using XL-MS data. For conformer selection, w...
ORGANISM(S): Escherichia coli 
2024-05-24 | PXD046392 | Pride
Crosslinks Monolinks Alphafold2 Idr Flexible protein 
UnknownMono- and Intralink Filter (Mi-Filter) To Reduce False Identifications in Cross-Linking Mass Spectrometry Data.
Not available
S-EPMC9798375 | biostudies-literature
Proteomics26S proteasome crosslinking mass spectrometry data for mi-filter
In this project we are describing a novel mono- and intralink filter (mi-filter) that is applicable to any kind of crosslinking data and workflow. It stipulates that only proteins for which at least one monolink or intra-protein crosslink has been identified within a given dataset are considered for...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2022-12-14 | PXD031215 | Pride
26s proteasome Mi-filter Crosslinking mass spectrometry 
UnknownRational Modification of a Cross-Linker for Improved Flexible Protein Structure Modeling.
Not available
S-EPMC11755394 | biostudies-literature
UnknownModeling Flexible Protein Structure With AlphaFold2 and Crosslinking Mass Spectrometry.
Not available
S-EPMC10884514 | biostudies-literature
ProteomicsRNxQuest: an extension to the xQuest pipeline enabling analysis of protein-RNA cross-linking/mass spectrometry data
The recently introduced cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) technique enables protein-RNA cross-links to be used as precisely localized distance restraints in de novo structural modelling. The novel data type requires a bespoke data analysis approach. The n...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) 
2023-09-06 | PXD039754 | Pride
Uv cross-linking  mbnl1  fox1  ptbp1  bsa  cross-linking  xl-ms  structural proteomics  protein-rna  rna-protein  protein-rna complex  rna-protein complex  clir-ms 
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 
ProteomicsMavacamten inhibits myosin activity by stabilising the myosin interacting-heads motif and stalling motor force generation
Most sudden cardiac deaths in young people arise from hypertrophic cardiomyopathy, a genetic disease of the heart muscle, with many causative mutations found in the molecular motor beta-cardiac myosin that drives contraction. Therapeutic intervention for hypertrophic cardiomyopathy has until recentl...
ORGANISM(S): Mus musculus (Mouse) Homo sapiens (Human) 
2026-03-26 | PXD059316 | Pride
Dsbu Skyline Cardiac myosin Quantitative crosslinking ms 
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 
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