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ProteomicsAn experimentally generated peptide database increases the sensitivity in XL-MS of complex samples
The application of non-cleavable cross-linkers to complex samples in XL-MS workflows is limited by the n² problem, a quadratic expansion of the search space with increasing database size. Here, a peptide-focused approach is proposed, for which cross-linking peptide candidates are identified in a par...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2020-03-26 | PXD016554 | Pride
Peptide database Xl-ms 20 s proteasome Bacillus subtilis Polii Cross-linking Tfiih Bacillus cereus 
ProteomicsA deep XL-proteomic dataset of intact HEK293T cells using DSBSO
Cross-linking mass spectrometry is an emerging method to study protein-protein interactions (PPIs) in intact biological systems. Here, we optimized a workflow for gnerating high coverage maps of PPIs using the enrichable cross-linker Azide-A-DSBSO. This created one of the largest to-date XL-MS datas...
ORGANISM(S): Homo sapiens (Human) 
2024-10-17 | PXD043531 | Pride
Human Deep xl-ms Cell culture 
TranscriptomicsDeciphering the ghost proteome in ovarian cancer cells by deep proteogenomic characterization
Proteogenomics is becoming a powerful tool in personalized medicine by linking genomics, transcriptomics and mass spectrometry (MS)-based proteomics. Due to increasing evidence of alternative open reading frame-encoded proteins (AltProts), proteogenomics has a high potential to unravel the character...
ORGANISM(S): Homo sapiens 
2023-11-17 | GSE248039 | GEO
UnknownAIRPred: A Deep Learning Model Predictor for Peptide Intensity Ratios in Cross-Linking Mass Spectrometry Improves Cross-Link Spectrum Matching.
Not available
S-EPMC12658862 | biostudies-literature
ProteomicsXL-MSDigger: A Computational Pipeline for In-Depth Data Analysis and Mining of Cross-Linking Mass Spectrometry
Cross-linked mass spectrometry (XL-MS) plays an increasing role in the study of protein structure and protein-protein interactions, but the development of its data analysis methods is currently lagging that of conventional proteomics, especially in terms of artificial intelligence-based analysis and...
ORGANISM(S): Homo Sapiens 
2025-04-23 | PXD063217 |
ProteomicsA high-efficiency Azide-A-DSBSO cross-linking-MS protocol for identifying thousands of in vivo protein interactions in single day
Enrichable and mass spectrometry (MS)-cleavable crosslinkers have gained popularity in crosslinking-MS (XL-MS) in the past decade. The azide-tagged, acid-cleavable disuccinimidyl bis-sulfoxide (DSBSO) crosslinker offers both these advantages, enabling deep XL-MS interactomics studies in intact cells...
ORGANISM(S): Homo sapiens (Human) Bacillus subtilis 
2025-11-27 | PXD065905 | Pride
High-thoughput Cross-linking mass spectrometry Dsbso 
GenomicsDeciphering the ghost proteome in ovarian cancer cells by deep proteogenomic characterization
Deciphering the ghost proteome in ovarian cancer cells by deep proteogenomic characterization
PRJNA1041444 | ENA
ProteomicsExpanding the depth and sensitivity of cross-link identification by differential ion mobility using FAIMS
In cross-linking mass spectrometry (XL-MS), the depth and sensitivity of cross-link detection is often limited by the low abundance of cross-links compared to non-cross-linked peptides in the digestion mixture. To improve the identification efficiency of cross-links, here we present a gas-phase sepa...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) Gallus gallus (Chicken) Equus caballus (Horse) 
2020-07-22 | PXD019926 | Pride
Faims Whole proteome Cross-linking mass spectrometry Xl-ms Orbitrap fusion lumos Cx-ms 
UnknownPhoXplex: Combining Phospho-enrichable Cross-Linking with Isobaric Labeling for Quantitative Proteome-Wide Mapping of Protein Interfaces.
Not available
S-EPMC11537259 | biostudies-literature
ProteomicsDeciphering the ghost proteome in ovarian cancer cells by deep proteogenomic characterization.
Proteogenomics is becoming a powerful tool in personalized medicine by linking genomics, transcriptomics, and mass spectrometry (MS)-based proteomics. Due to increasing evidence of alternative open reading frame-encoded proteins (AltProts), proteogenomics has high potential to unravel the characteri...
ORGANISM(S): Homo sapiens (Human) 
2025-05-06 | PXD045689 | Pride
Alternative proteins Proteogenomics Ovarian cancer Crosslinking 
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