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ProteomicsXL-MS data analysis with MeroX and XlinkX
Comparison of MeroX in different modes and XlinkX upon variation of database size based on DSBU linked BSA as test-dataset
ORGANISM(S): Bos taurus (Bovine) 
2020-11-17 | PXD021648 | Pride
Mass-spectromerty Dsbu Xlinkx Merox Crosslinking Bsa 
UnknownA Workflow for Improved Analysis of Cross-Linking Mass Spectrometry Data Integrating Parallel Accumulation-Serial Fragmentation with MeroX and Skyline.
Not available
S-EPMC11099889 | biostudies-literature
ProteomicsPeptide centric detection of cross-linked peptides using PASEF, MeroX, and Skyline
Cross-linking mass spectrometry (XL-MS) has evolved into a pivotal technique for probing protein interactions, with recent ad-vancements significantly enhancing its analytical potential. This technical note presents advancements in cross-linking mass spec-trometry (XL-MS) through the implementation ...
ORGANISM(S): Bos Taurus 
2024-05-13 | PXD047307 | panorama
ProteomicsA Simple Cross-Linking/Mass Spectrometry Workflow to Study System-Wide Protein Interactions in Drosophila Embryos
We provide a cross-linking/MS workflow that can be applied to complex systems. The software tool MeroX 2.0 can be used to identify cross-linked peptide on a proteome-wide level. We applied the workflow to extracts of Drosophila embryos and identified 5,129 unique cross-linked residue pairs in biolog...
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2019-07-09 | PXD012546 | Pride
Cross-linking Mass spectrometry Xlms Cxms Drosophila 
ProteomicsCrosslinking mass spectrometry dataset for mzIdentML 1.3 validation with MeroX 2.0.2.5
This dataset was generated to support the validation of mzIdentML 1.3 files, including the crosslinking extension. The dataset contains LC-MS/MS data and crosslinking search results for DSBU-crosslinked peptides, together with mzIdentML 1.3 files containing crosslinking-specific annotations and cont...
ORGANISM(S): Homo sapiens (Human) 
2026-06-03 | PXD077188 | Pride
Xl-ms Mzidentml 
ProteomicsDetermining TCR Binding Orientation and Peptide-HLA Interac-tions Using Cross-Linking Mass Spectrometry
T cell receptors (TCRs) recognize specific peptides presented by human leukocyte antigens (HLAs) on the surface of antigen presenting cells and are involved in fighting pathogens and cancer surveillance. Canonical docking orientation of TCRs to their target peptide-HLAs (pHLAs) is essential for T ce...
ORGANISM(S): Escherichia coli 
2025-05-07 | PXD056652 | Pride
Lc-ms/ms Cross-linking 
ProteomicsDevelopment of Photocrosslinking Probes Based on Huwentoxin-IV to Map the Site of Interaction on Nav1.7
This study reports on the design of a library of photoprobes based on the potent spider toxin Huwentoxin-IV and the determination of the toxin binding interface on VSD2 of Nav1.7 through a photocrosslinking and tandem mass spectrometry approach. Our Huwentoxin-IV probes selectively crosslink to extr...
ORGANISM(S): Homo sapiens (Human) 
2019-11-18 | PXD015037 | Pride
Nav1.7 Photoaffinity labelling Huwentoxin-iv Diazirine Peptide mapping 
ProteomicsComprehensive identification of crosslinked peptides from methyltransferase Hmt1 and its substrate Npl3: use of multiple crosslinkers, mass spectrometry approaches and software platforms
Chemical-Crosslinking Mass Spectrometry (XLMS) using MS-cleavable crosslinkers is fast becoming an established technique in the study of protein-protein interactions for both small and large scale samples. With the increased uptake of XLMS as a technique, different combinations of crosslinker types,...
ORGANISM(S): Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2018-07-20 | PXD008348 | Pride
Crosslinking-mass spectrometry Ms-cleavable linkers 
ProteomicsMimicked synthetic ribosomal protein complex for benchmarking cross-linking mass spectrometry workflows
The field of cross-linking mass spectrometry has matured to a frequently used tool for the investiga-tion of protein structures as well as interactome studies up to a system wide level. The growing com-munity generated a broad spectrum of applications, linker types, acquisition strategies and specia...
ORGANISM(S): Escherichia coli 
2022-05-24 | PXD029252 | Pride
Mass spectrometry Ribosome Fdr Crosslinking 
ProteomicsCross-linking mass spectrometry analyses of three different kinetochore protein complexes (KMN, NDC80C, MIS12C) using an MS-cleavable cross-linker, BuUrBu (DSBU)
In order to develop a simplified cross-linking mass spectrometry protocol, we applied one-step size-exclusion chromatography (SEC) for peptide purification after proteolysis with Lys-C and trypsin. Three benchmark protein complexes (KMN, NDC80C, MIS12C) from human kinetochore were cross-linked with ...
ORGANISM(S): Homo sapiens (Human) 
2019-04-01 | PXD010070 | Pride
Dsbu Q-exactive Cross-linking ms Buurbu Merox Human Kinetochore Protein complex Ms-cleavable cross-linker 
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