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ProteomicsIdentify Yeast Proteasome Cross-links with Multiple Ion Fragmentation Methods
Use of EThcD, CID, HCD and high energy HCD to identify protein cross-links
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2020-06-18 | PXD018310 | Pride
Yeast Proteasome Cross-links 
ProteomicsIdentification of Native Cross-links in Bacillus subtilis Spore Coat Proteins
The resistance properties of the bacterial spores are partially due to spore surface proteins, ~30% of which are said to form an insoluble protein fraction. Previous research has also identified a group of spore coat proteins affected by spore maturation, which exhibit an increased level of inter pr...
ORGANISM(S): Bacillus Subtilis (ncbitaxon:1423) 
2021-01-09 | MSV000086681 | MassIVE
ProteomicsReal-time library search assisted identification of cross-links increases resolution for structural modeling and interactome mapping
Cross-linking mass spectrometry (XL-MS) is a universal tool of molecular and structural biology for probing structural dynamics and protein-protein interactions in vitro and in vivo. Although cross-linked peptides are naturally less abundant than their unlinked counterparts, recent experimental adva...
ORGANISM(S): Escherichia coli 
2023-03-20 | PXD037652 | Pride
Rtls E coli Cross-linking Diagnostic peaks Xl-ms Phox 
ProteomicsIntensity and retention time prediction improves the rescoring of protein-nucleic acid cross-links
Rescoring of protein-RNA cross-links using retention time and intensity prediction.
ORGANISM(S): Escherichia coli 
2025-11-24 | PXD048145 | Pride
Lc-msms Protein-rna cross-links Bottom-up proteaomics 
ProteomicsStructural Analysis of a Prokaryotic Ribosome Using a Novel Amidinating Cross-Linker and Mass Spectrometry
The structure of the Escherichia coli ribosome, a 2.5 MDa ribonucleoprotein complex containing more than 50 proteins, was probed using the novel amidinating cross-linker diethyl suberthioimidate (DEST) and mass spectrometry. Peptide cross-links derived from this complex structure were identified at ...
ORGANISM(S): Escherichia coli 
2015-12-23 | PXD003381 | Pride
Amidination Dest E. coli Mass spectrometry Diethyl suberthioimidate Ribosome Protein cross-linking 
ProteomicsProteome-wide identifying site non-specific cross-linking peptides with SpotLink
We developed SpotLink to identify site non-specific cross-links from the proteome scale. Here described the Abeta dataset and the HeLa dataset to evaluate SpotLink.
ORGANISM(S): Homo sapiens (Human) 
2022-08-25 | PXD030274 | Pride
Spotlink Cross-linking Cx-ms Site non-specific Cl-ms Proteome 
ProteomicsDithiothreitol (DTT) acts as a specific, UV-inducible cross-linker in elucidation of protein-RNA interactions
In the present paper, we introduce dithiothreitol (DTT) as a potent protein-RNA cross-linker. To prove this three model systems, a) a small synthetic peptide from smB'/B protein incubated with U1snRNA oligonucleotide, b) in vitro reconstituted 15.5K protein with U4 snRNA oligonucleotide and c) nativ...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2022-03-01 | PXD002392 | Pride
Dtt Protein-rna cross-links 
ProteomicsCharacterizing the dynamic oligomerization of Hsp90β using photo-cross-linking
Cross-linking mass spectrometry (XL-MS) is a powerful tool for probing protein structures. While conventional chemical cross-linkers react with specific residues with defined chemistry, photo-cross-linkers, despite their superior reactivity, have been hindered by incomplete mechanistic understanding...
ORGANISM(S): Homo sapiens (Human) 
2026-04-09 | PXD072009 | Pride
Hsp90 Cleavable cross-linkers Diazirine Photo-cross-linking 
ProteomicsOptimized fragmentation improves the identification of peptides cross-linked using MS-cleavable reagents
Cross-linking mass spectrometry (XLMS) is becoming increasingly popular, and current advances are widening the applicability of the technique so that it can be utilized by non-specialist laboratories. Specifically, the use of novel mass spectrometry-cleavable (MS-cleavable) reagents dramatically red...
ORGANISM(S): Bos taurus (Bovine) Cicer arietinum (Chickpea) (Garbanzo) Streptococcus pyogenes serotype M2 Candida albicans (Yeast) Homo sapiens (Human) Oryctolagus cuniculus (Rabbit) Escherichia coli Equus caballus (Horse) 
2019-02-01 | PXD011861 | Pride
Xlms Cross-linking Cleavable cross-linking reagents Dsso Stepped-hcd 
ProteomicsThe Fanconi anemia pathway repairs colibactin-induced DNA interstrand cross-links
Colibactin is a secondary metabolite produced by bacteria present in the human gut and is implicated in the progression of colorectal cancer and inflammatory bowel disease. This genotoxin alkylates deoxyadenosines on opposite strands of host cell DNA to produce DNA interstrand cross-links (ICLs) tha...
ORGANISM(S): Xenopus laevis (African clawed frog) 
2025-09-11 | PXD055646 | Pride
Interstrand cross-link Colibactin Xenopus laevis 
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