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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 
UnknownHistone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei.
Not available
S-EPMC6166682 | biostudies-literature
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 
UnknownChemical crosslinking extends and complements UV crosslinking in analysis of RNA/DNA nucleic acid-protein interaction sites by mass spectrometry.
Not available
S-EPMC12359043 | biostudies-literature
ProteomicsAlphaLink: bringing protein structure prediction in situ with in-cell photo-crosslinking mass spectrometry, crosslinking mass spectrometry, XL-MS,
The protein structure prediction problem has been revolutionised by AlphaFold2, an algorithm that uses neural networks and evolutionary information to predict accurate models from the primary sequence. However, some proteins remain difficult to predict. Moreover, proteins are dynamic entities that e...
ORGANISM(S): Escherichia Coli 
2023-02-22 | PXD036833 | JPOST Repository
UnknownModeling Protein Complexes Using Restraints from Crosslinking Mass Spectrometry.
Not available
S-EPMC6039719 | biostudies-literature
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 
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 
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 
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