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ProteomicsFAIMS-GPF XL-MS: crosslinking-mass spectrometry based on gas-phase fractionation
Protein-protein interactions (PPIs) underpin nearly all cellular processes; therefore, mapping PPI and protein-protein association networks is critical for understanding how biological systems function in health and disease. However, many functionally relevant PPIs are transient and mediated by weak...
ORGANISM(S): Homo sapiens (Human) 
2026-05-27 | PXD064228 | Pride
Faims Cross-linking mass spectrometry Structural biology Interactomics 
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 
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 
ProteomicsMapping the Toxoplasma gondii cytosolic interactome by crosslinking mass spectrometry and machine learning
Protein–protein interactions (PPIs) are fundamental to cellular processes and pathogen biology, yet remain undercharacterized in the human parasite Toxoplasma gondii. Here, we apply crosslinking mass spectrometry (XL-MS) to map the cytosolic interactome of T. gondii tachyzoites at proteome scale. Us...
ORGANISM(S): Toxoplasma gondii type I 
2025-07-26 | PXD062479 | Pride
Machine learning Cytosol Protein–protein interactions Dense granule proteins Crosslinking mass spectrometry Interactome Dsbso Host-pathogen interactions Structural mapping Toxoplasma gondii Lightgbm Parasite proteomics Ribosome Proteasome 
ProteomicsChanges in the ATP synthase interactome in mitochondrial dysfunction by crosslinking mass spectrometry
Mitochondrial oxidative phosphorylation (OXPHOS) comprises a series of multi-subunit protein complexes that operate in coordination with the tricarboxylic acid (TCA) cycle to generate ATP. Although these systems are metabolically interconnected, complex II is generally regarded as the only direct st...
ORGANISM(S): Mus musculus (Mouse) 
2026-05-18 | PXD071441 | Pride
Atp synthase  mitochondrial dysfunction  tca cycle  crosslinking mass spectrometry  oxphos 
ProteomicsCrosslinking mass spectrometry unveils novel interactions and structural distinctions in the model green alga Chlamydomonas reinhardtii
Interactomics is an emerging field that seeks to identify both transient and complex-bound protein interactions that are essential for metabolic functions. Crosslinking mass spectrometry (XL-MS) has enabled untargeted global analysis of these protein networks, permitting largescale simultaneous anal...
ORGANISM(S): Chlamydomonas reinhardtii 
2021-11-03 | PXD026433 | Pride
Chlamydomonas Photosynthesis Crosslinking mass spectrometry Interactome Lc-ms/ms 
ProteomicsBreaking Barriers in Crosslinking Mass Spectrometry: Enhanced Throughput and Sensitivity with the Orbitrap Astral Mass Analyzer
Crosslinking mass spectrometry (XL-MS) has become a key technique for investigating protein-protein interactions and the architecture of biological systems. This study compares the Orbitrap Astral and Eclipse mass spectrometers in XL-MS workflows, emphasizing their performance in detecting low-abund...
ORGANISM(S): Homo sapiens (Human) 
2025-12-15 | PXD059096 | Pride
Crosslinking mass spectrometry Fragmentation Orbitrap eclipse Hcd Quality control Compensation voltage Orbitrap astral 
ProteomicsThe ubiquitin-like modifier FAT10 interferes with SUMO activation
In this study, the proteins SumoE1 and Fat10 or Fat10-AV mutant were crosslinked using the crosslinking reagent H12/D12 BS3 in order to determine specific interaction sites of Fat10 and SumoE1. Furthermore, quantitative chemical crosslinking coupled to mass spectrometry (q-XL-MS) was used to compare...
ORGANISM(S): Homo sapiens (Human) 
2019-10-08 | PXD012592 | Pride
Fat10 Q-xl-ms Xl-ms Sumoe1 
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 
ProteomicsEarly Scanning of Nascent Polypeptides inside the Ribosomal Tunnel by NAC
In this study, NAC was UV-crosslinked using the photo-crosslinking amino acid p-benzoyl-L-phenylalanine (pBPA) in order to determine specific interaction sites of the alphaNAC N-terminus in the native protein structure. Furthermore, quantitative chemical crosslinking coupled to mass spectrometry (q-...
ORGANISM(S): Homo sapiens (Human) Caenorhabditis elegans 
2019-07-25 | PXD011995 | Pride
Nac Structural mass spectrometry Uv-crosslinking Q-xl-ms 
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