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ProteomicsA synthetic crosslinked peptide library for benchmarking crosslinking mass spectrometry search engines
We have created a synthetic crosslinked peptide library to benchmark crosslinking mass spectrometry search engines. The unique benefit of the library is knowing which identified crosslinks are true and which are false. The data collected from mass spectrometry measurements of the peptide library wer...
ORGANISM(S): Streptococcus pyogenes ABC020006030 
2020-07-28 | PXD014337 | Pride
Crosslinking mass spectrometry peptide library 
ProteomicsQuantitative photo-crosslinking mass spectrometry reveals protein structure response to environmental changes
Conformational changes of protein structures depend on their chemical and physical environment. Studying conformational changes depending on environmental parameters is notoriously difficult as many methods of structural biology are affected by parameters like temperature or pH. To make such conform...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) 
2019-07-01 | PXD012939 | Pride
Data-independent acquisition Structural dynamics Human serum albumin Dia-qclms Quantitation Xi Cytochrome c Spectronaut Label-free Mass spectrometry Photo-crosslinking Cross-linking Sda 
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 
ProteomicsMapping protein-DNA interactions by UV femtosecond laser crosslinking and mass spectrometry analysis
Transcription factors (TFs) regulate target genes by specific interaction with DNA sequences. Detecting and understanding these interactions on molecular level is of fundamental interest in both biological and clinical context. Crosslinking mass spectrometry is a powerful tool to assist structure pr...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) Sus scrofa domesticus (domestic pig) 
2020-06-22 | PXD014898 | Pride
Femtosecond laser Uv Transcription factor Protein-dna crosslinking Mass spectrometry 
ProteomicsIn Situ Structural Restraints from Crosslinking Mass Spectrometry in Human Mitochondria
The field of structural biology is increasingly focusing on studying proteins in situ, i.e. in a larger biological context. Crosslinking mass spectrometry is contributing to this effort, typically through the use of MS-cleavable crosslinkers. Here, we apply the popular non-cleavable crosslinker disu...
ORGANISM(S): Homo sapiens (Human) 
2019-12-03 | PXD014675 | Pride
Crosslinking mass spectrometry Human mitochondria In situ large-scale structural biology Non-cleavable dss crosslinker Comparative modelling 
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 
ProteomicsCrosslinking mass spectrometry analysis of 𝛾TuRC complex
The 𝛾-tubulin ring complex (𝛾TuRC) is the major microtubule nucleator in cells. The mechanism of its regulation is not understood. To understand the molecular basis of microtubule nucleation, we investigate the structure of 𝛾TuRC using crosslinking mass spectrometry.
ORGANISM(S): Homo sapiens (Human) 
2021-01-27 | PXD018106 | Pride
Integrative structural analysis Crosslinking mass spectrometry 𝛾turc complex 
ProteomicsMass spectrometry approach to identify mitochondrial poly(A) RNA interacting proteins
To identify mitochondrial RNA-interacting proteins, we developed three related mass spectrometry based methods. In the first method, called mitochondrial crosslinking (MXL), mitochondria of 4-thiouridine labelled cells were isolated, exposed to UV-light and poly(A) RNA was isolated. In the second me...
ORGANISM(S): Homo sapiens (Human) 
2019-10-15 | PXD014957 | Pride
Mitochondrial rna Mass spectrometry 4-thiouridine labelling & crosslinking 
ProteomicsMass spectrometry analysis of chromosomal passenger complex proteins and kinetochore proteins in Trypanosoma brucei
We performed chemical crosslinking mass spectrometry of native protein complexes purified from Trypanosoma brucei procyclic cells to obtain protein-protein interaction information for the chromosomal passenger complex (CPC) and kinetochore complex. Crosslinks among CPC subunits were detected using Y...
ORGANISM(S): Trypanosoma brucei 
2023-10-13 | PXD045987 | Pride
Kinetochore 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 
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