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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 
ProteomicsEnhanced Proteomics Analysis with a Novel Recombinant Chymotrypsin Analogue En-gineered for High Cleavage Specificity
Chymotrypsin is widely used in shotgun proteomics owing to its orthogonal cleavage specificity relative to trypsin, which enhances sequence coverage of hydrophobic protein regions. However, commercial preparations often display variable cleavage specificity, trypsin contamination, and elevated misse...
ORGANISM(S): Homo sapiens (Human) 
2026-06-08 | PXD072165 | Pride
Chymotrypsin Missed cleavages Sample preparation Proteomics Protein digestion 
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 
ProteomicsDual FAN1 activities stabilize the HTT CAG repeat
Recent data strongly suggest HTT CAG repeat expansion drives Huntington’s disease (HD) pathogenesis and that disease development is modulated by components of the DNA damage response (DDR) pathway. FAN1 has been identified as a major HD modifier which slows expansion of the HTT CAG repeat in several...
ORGANISM(S): Homo sapiens (Human) 
2022-02-16 | PXD023221 | Pride
Crosslinking Fan1 
ProteomicsIntermittent bulk release of human cytomegalovirus
Human Cytomegalovirus (HCMV) significantly remodels host cell processes and membranes to enable effective production of virus progeny. Nascent capsids exit the nucleus and undergo a final morphogenesis process in the cytoplasm where they associate with tegument and membranes. During this process ca...
ORGANISM(S): Human cytomegalovirus (HHV-5) (Human herpesvirus 5) 
2022-06-23 | PXD023444 | Pride
Cellular egress Human cytomegalovirus Morphogenesis Integrative microscopy 
ProteomicsQToF Cross-linking Optimisation
Optimising the parameters for cross-link analysis using a QToF mass spectrometer. We performed triplicate analysis of 6 different collision energy ramps to determine the optimal energy for cross-link fragmentation.
ORGANISM(S): Bos taurus (Bovine) 
2019-11-12 | PXD011704 | Pride
Bsa lc-ms/ms cross-linking 
ProteomicsDynamic changes in the brain protein interaction network correlates with progression of Aβ42 pathology in Drosophila
Alzheimer’s disease (AD), the most prevalent form of dementia, is a progressive and devastating neurodegenerative condition for which there are no effective treatments. Understanding the molecular pathology of AD during disease progression may identify new ways to reduce neuronal damage. Here, we pr...
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2020-12-08 | PXD015443 | Pride
Brain Drosophila Aβ42 pathology Interaction network 
ProteomicsFormation of ER-lumenal intermediates during export of Plasmodium proteins containing transmembrane-like hydrophobic sequences
REX3RQLSE:Pf332:C-S11:DSLE is exported and is diffusely localised in the red blood cell cytoplasm (Fig 3A). Mutation of the PEXEL sequence (REX3AQLSE:Pf332:C-S11:DSLE), results in the protein being retained in the parasite (Fig 3C), and addition of a C-terminal SDEL sequence (REX3RQLSE:Pf332:C-S11:S...
ORGANISM(S): Plasmodium falciparum 
2023-03-28 | PXD036904 | Pride
Plasmodium Proteomics Lc-ms/ms 
ProteomicsMacrocycle-based PROTACs selectively degrade cyclophilin A and inhibit HIV-1 and HCV
We have designed and characterised antiviral PROteolysis TArgeting Chimeras (PROTACs) targeting the human protein cyclophilin A (CypA), a host cofactor for unrelated viruses including human immunodeficiency virus (HIV) and hepatitis C virus (HCV). The PROTAC warheads are based on fully synthetic mac...
ORGANISM(S): Homo sapiens (Human) 
2024-11-29 | PXD057024 | Pride
Proteomics Dia Hiv Protac 
Proteomicsrotein expression in Nav1.7 embryonic null mice – mechanisms of compensation
Mice and humans who have lost the expression of functional sodium channel Nav1.7 are pain-free, but otherwise normal. This is the result of a loss of neurotransmitter release such as glutamate and Substance P from primary sensory neurons. The sensory neurons are otherwise normal apart from loss of n...
ORGANISM(S): Mus musculus (Mouse) 
2024-10-17 | PXD052513 | Pride
Two mechanisms of analgesia Drugs Pain Humans Autonomic side-effects Embryonic and adult nulls Sodium channels Mice Nav1.7 Opioid signalling 
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