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ProteomicsReal-time library search assisted identification of cross-links increases resolution for structural modeling and interactome mapping
Cross-linking mass spectrometry (XL-MS) is a universal tool of molecular and structural biology for probing structural dynamics and protein-protein interactions in vitro and in vivo. Although cross-linked peptides are naturally less abundant than their unlinked counterparts, recent experimental adva...
ORGANISM(S): Escherichia coli 
2023-03-20 | PXD037652 | Pride
Rtls E coli Cross-linking Diagnostic peaks Xl-ms Phox 
ProteomicsEnergy transfer photoproximity labelling in live cells using an organic cofactor
Photocatalytic proximity labelling has recently emerged as a powerful tool to resolve a wide variety of biomolecular and cellular interactions. While the use of high-resolution probe species, such as diazirines, enables cell-surface protein labelling with nanometre precision by generating highly rea...
ORGANISM(S): Homo sapiens (Human) 
2025-12-08 | PXD056778 | Pride
Photoproximity Diazirine Lfq Dart 
ProteomicsDeciphering Membrane Protein Complexes in Plasmodium falciparum Gametocytes via Cross-Linking Mass Spectrometry and Structural Modeling
Malaria is a disease targeting the most vulnerable people. It is caused by the parasite Plasmodium falciparum, and is transmitted to humans by Anopheles mosquitos during a blood meal, who are in turn infected by the parasite if they feed on an infected human. While current eradication efforts focus ...
ORGANISM(S): Plasmodium falciparum 58.1 Homo sapiens (Human) 
2026-04-09 | PXD067699 | Pride
Gametocytes Malaria Cross-linking Plasmodium Alphafold 
ProteomicsDataset used to guide the development of Scout and bechmark XL-MS search engines
This submission includes the raw data analyzed and search results described in our manuscript “Proteome-Scale Recombinant Standards And A Robust High-Speed Search Engine To Advance Cross-Linking MS-Based Interactomics”. In this study, we develop a strategy to generate a well-controlled XL-MS standar...
ORGANISM(S): Homo sapiens (Human) 
2024-08-03 | PXD052022 | Pride
Search engine Cross-linking Ppi Benchmarking Xl-ms Fdr 
ProteomicsDeazaflavin-Diazirine Energy-Transfer (DarT) Photoproximity Labelling of the HER2 Interactome Using Antibody Conjugates
Elucidating protein-protein interactions plays a crucial part in understanding disease mecha-nisms and advancing pharmacological research. Photocatalytic proximity labelling using anti-body–catalyst conjugates enables the highly target-specific analysis of protein-protein inter-actions on the cell s...
ORGANISM(S): Homo sapiens (Human) 
2026-08-04 | PXD076830 | Pride
ProteomicsAn Uncommon Phosphorylation Mode Regulates the Activity and Protein Interactions of N-Acetylglucosamine Kinase
Reversible protein phosphorylation serves as a pivotal signaling mechanism in eukaryotic cells, contrasting with the poorly understood protein pyrophosphorylation, a posttranslational modification (PTM) whose functions in living organisms remain elusive. Unlike kinase-mediated protein phosphorylatio...
ORGANISM(S): Homo sapiens (Human) 
2024-05-22 | PXD049339 | Pride
Pulldown Affinity-purification ms Lfq Phosphorylation Pyrophosphorylation 
ProteomicsNucleoside diphosphate kinase A (NME1) catalyzes its own oligophosphorylation
Protein phosphorylation is a central regulatory mechanism in eukaryotic cell signaling, and was recently expanded to include protein pyrophosphorylation and protein polyphosphorylation. Here, we report the discovery of yet another mode of phosphorylation – protein oligophosphorylation. Using site-sp...
ORGANISM(S): Homo sapiens (Human) 
2025-08-21 | PXD054175 | Pride
Oligophosphorylation Open-search Phosphorylation 
ProteomicsUnsaturated phosphorus electrophiles to probe protein tyrosine phosphatases
Protein tyrosine phosphatases (PTPs) represent an important pharmacological target. To this end, broad spectrum electrophilic, phosphotyrosine-mimicking probes have been developed to covalently capture the catalytic site of these enzymes. Despite these efforts, there is still a high demand for synth...
ORGANISM(S): Homo sapiens (Human) 
2026-03-03 | PXD068999 | Pride
ProteomicsQ2C: A Software for Managing Mass Spectrometry Facilities
We present Q2C, an open-source software designed to streamline mass spectrometer queue management and assess performance based on quality control metrics. Q2C provides a fast and user-friendly interface to visualize projects queues, manage analysis schedules and keep track of samples that were alrea...
ORGANISM(S): Homo sapiens (Human) 
2025-08-21 | PXD055186 | Pride
Quality control Software 
ProteomicsOptimized TMT-based quantitative cross-linking mass spectrometry strategy for large-scale interactomic studies
Cross-linking mass spectrometry is a powerful method for the investigation of protein-protein interactions from highly complex samples. XL-MS combined with tandem mass tag labeling holds the promise of large-scale PPI quantification. However, a robust and efficient TMT-based XL-MS quantification met...
ORGANISM(S): Homo sapiens (Human) Escherichia coli Bacteria 
2022-04-07 | PXD031114 | Pride
Faims Hek Ratio distortion E. coli Mass spectrometry Lumos Dsso Xl-ms Interactome Stepped hcd Cross-linking Interference Sps 
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