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Proteomics4D-diaXLMS: Proteome-wide Four-Dimensional Data-Independent Acquisition Workflow for Cross-linking Mass Spectrometry
Cross-linking Mass Spectrometry (XL-MS) is a powerful tool for examining protein structures and interactions. Nevertheless, anal-ysis of low-abundance cross-linked peptides is often limited in data-dependent acquisition (DDA) mode due to its semistochastic nature. To address this issue, we introduce...
ORGANISM(S): Homo Sapiens Saccharomyces Cerevisiae 
2023-06-26 | PXD043282 |
ProteomicsProteome-Wide Photo-Crosslinking Enables Residue-Level Visualization of Protein Interaction Networks in vivo
Crosslinking mass spectrometry (XL-MS) is emerging as a unique method at the crossroads of structural and cellular biology, uniquely capable of identifying protein-protein interactions with residue-level resolution and on the proteome-wide scale. With the development of crosslinkers that can form li...
ORGANISM(S): Escherichia coli 
2023-12-07 | PXD036884 | Pride
Heterobifunctional crosslinker Escherichia coli Xl-ms Diazirine Cleavable crosslinker Photo-crosslinking Proteome-wide Nhs-carbamate 
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 
ProteomicsProteome-wide cross-linking mass spectrometry of human K562 cells
Proteome-wide cross-linking mass spectrometry was performed on human K562 cell lysates. MS2-MS3 fragmentation strategy was used to aquire the XL-MS data. The raw files in this dataset are a subset of PXD013928.
ORGANISM(S): Homo sapiens (Human) 
2020-07-01 | PXD018771 | Pride
Human Protein-protein Cross-linking mass spectrometry Proteome-wide Interaction 
UnknownDSBSO-Based XL-MS Analysis of Breast Cancer PDX Tissues to Delineate Protein Interaction Network in Clinical Samples.
Not available
S-EPMC11296914 | biostudies-literature
ProteomicsOptimized parameter settings enhance proteome-wide formation of crosslinks on low-abundant proteins
Studies using crosslinking coupled to mass spectrometry on the proteome-wide level have spurred great interest as they facilitate structural probing of protein interactions in living cells or even organisms. Here we show, by using both an in-vitro mimic of a crowded cellular environment and eukaryot...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2020-02-17 | PXD014759 | Pride
Proteome-wide xl-ms Reaction kinetics 
UnknownStructure-based validation can drastically underestimate error rate in proteome-wide cross-linking mass spectrometry studies.
Not available
S-EPMC7534832 | biostudies-literature
UnknownTwo-Dimensional Fractionation Method for Proteome-Wide Cross-Linking Mass Spectrometry Analysis.
Not available
S-EPMC9056026 | biostudies-literature
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 
UnknownExploring an Alternative Cysteine-Reactive Chemistry to Enable Proteome-Wide PPI Analysis by Cross-Linking Mass Spectrometry.
Not available
S-EPMC10284117 | biostudies-literature
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