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ProteomicsLiP-Quant, an automated chemoproteomic approach to identify drug targets in complex proteomes
Chemoproteomics is a key technology to characterize the mode of action of drugs, as it directly identifies the protein targets of bioactive compounds and aids in developing optimized leads. We have developed a drug target deconvolution approach with an automated data analysis pipeline, based on limi...
ORGANISM(S): Homo sapiens (Human) Botryotinia fuckeliana (Noble rot fungus) (Botrytis cinerea) Saccharomyces cerevisiae (Baker's yeast) 
2020-09-09 | PXD015446 | Pride
Limited proteolysis Dia-ms Lip-ms Drug identification 
ProteomicsDetection of structure-specific protein–protein interactions of alpha-synuclein
Parkinson’s disease (PD) is a neurodegenerative disorder associated with the accumulation of intraneuronal protein aggregates called Lewy bodies. These inclusions contain aberrantly folded and aggregated alpha-synuclein (aSyn), a key protein involved in the pathology of PD, for which the mechanisms ...
ORGANISM(S): Homo sapiens (Human) 
2024-02-10 | PXD039784 | Pride
Amyloid fibrils Neurodegeneration Structural proteomics Protein-protein interactions Lc-msms Alpha-synuclein Interactome Induced pluripotent stem cell-derived cortical neurons Mass spectrometry Limited proteolysis Parkinson’s disease Proteomics Structure-specific interactions 
ProteomicsProbing antigen–antibody interactions using limited proteolysis–mass spectrometry
Protein–protein interactions (PPIs) mediate multiple essential functions and regulatory events in living organisms. The physical interactome of a given protein can be abnormally altered in response to external and internal cues, thus modulating cell physiology and contributing to human pathologies i...
ORGANISM(S): Homo sapiens (Human) 
2024-02-10 | PXD039481 | Pride
Lc-msms Antibody-antigen interaction Interactome Mass spectrometry Respiratory syncytial virus fusion glycoprotein Limited proteolysis Structural proteomics Protein-protein interactions Mammalian cells Proteomics 
ProteomicsLimited proteolysis–mass spectrometry detects protein–protein interactions of integral membrane proteins
Integral membrane proteins (IMPs) are permanently embedded within the plasma membrane and execute multiple cellular functions. IMPs constitute important targets, but development of drugs that target IMPs to modulate protein–protein interactions, which mediate their functions, has been challenging. C...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) 
2024-02-10 | PXD039520 | Pride
Lc-msms Membrane proteins Interactome Mass spectrometry Limited proteolysis Structural proteomics Protein-protein interactions Proteomics Crude membranes 
ProteomicsAlpha-synuclein interacts with regulators of ATP homeostasis in mitochondria
Mitochondrial dysfunction and accumulation of α-synuclein aggregates are hallmarks of the neurodegenerative Parkinson’s disease and may be interconnected. In order to investigate the interplay between α-synuclein and brain mitochondria at near atomic structural level we applied NMR and identified α-...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) 
2025-07-18 | PXD063500 | Pride
Lip-ms Mitochondria Alpha-synuclein 
ProteomicsLimited proteolysis-coupled mass spectrometry captures proteome-wide protein structural alterations and biomolecular condensation in living cells
To study protein structures directly within cells, we developed in-cell limited proteolysis-coupled mass spectrometry (in-cell LiP-MS). Conditions for introduction of proteinase K into human cells using electroporation were optimized and validated for intracellular cleavages. In-cell LiP-MS captured...
ORGANISM(S): Homo sapiens (Human) 
2025-11-09 | PXD069095 | Pride
Stress granules Mass spectrometry In-cell lip Structural proteomics Limited proteolysis Arsenite treatment Rapamycin 
ProteomicsIn situ analysis of osmolyte mechanisms of proteome thermal stabilisation
Organisms across all kingdoms of life use small organic molecules called osmolytes to adapt to diverse environmental conditions and preserve viability. Osmolytes are thought to thermally stabilise proteins based on in vitro studies of a few purified proteins. The molecular mechanisms of osmolytes re...
ORGANISM(S): Escherichia coli 
2024-08-09 | PXD036186 | Pride
Osmolyte mechanisms Structural proteomics Stress adaptation Thermal stabilisation Aggregation 
ProteomicsGlobal, in situ analysis of the structural proteome in individuals with Parkinson’s disease to identify a new class of biomarker
Parkinson’s disease (PD) is a prevalent and incurable neurodegenerative disease for which robust biomarkers for early detection and tailored treatment are needed. Protein abundance measurements have so far not proven discriminative as PD biomarkers. Since alterations in protein structure reflect var...
ORGANISM(S): Homo sapiens (Human) 
2022-10-26 | PXD034120 | Pride
Human Parkinson disease Csf Structural proteomics Lc-ms/ms 
ProteomicsProteome-wide structural changes measured with 2 limited proteolysis-mass spectrometry: an advanced 3 protocol for high-throughput applications.
Proteins regulate biological processes by changing their structure or abundance to accomplish a specific function. In response to any perturbation or stimulus, protein structure may be altered by a variety of molecular events, such as post translational modification, protein-protein interaction, agg...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2023-01-10 | PXD031616 | Pride
Shotgun proteomics Human alpha-synuclein Yeast Structural proteomics Lip-ms 
ProteomicsDynamic 3D proteomes reveal functional pathway alterations in situ
Many biological processes are regulated via molecular events, such as intermolecular interactions and chemical modifications, which do not affect protein levels and escape detection in classical proteomic screens. Reasoning that these events affect protein structure, we propose here that a global pr...
ORGANISM(S): Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2020-11-02 | PXD022297 | Pride
Lc-msms Heat shock Metabolism Dia Limited proteolysis Structural barcodes Osmotic stress Dda Structure-function Shotgun proteomics 
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