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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 
UnknownEvaluation of Cleavable Crosslinking for Characterization of Proteoform Structural Differences by Top-Down Mass Spectrometry.
Not available
S-EPMC12798706 | biostudies-literature
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 
UnknownHistone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei.
Not available
S-EPMC6166682 | biostudies-literature
UnknownCharacterization of protein complexes in extracellular vesicles by intact extracellular vesicle crosslinking mass spectrometry (iEVXL).
Not available
S-EPMC9346492 | biostudies-literature
ProteomicsReliable identification of protein-protein interactions by crosslinking mass spectrometry_Protein coelution
Quantitative proteomics dataset on soluble, SEC-fractionated high-molecular weight proteome of E. coli for protein coelution analysis. This data was used to identify proteins for a subsequent crosslinking mass spectrometry search (DB creation) and to correlate protein elution behaviour to validate/...
ORGANISM(S): Escherichia Coli 
2021-04-14 | PXD019004 | JPOST Repository
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 
ProteomicsAlphaLink: bringing protein structure prediction in situ with in-cell photo-crosslinking mass spectrometry, crosslinking mass spectrometry, XL-MS,
The protein structure prediction problem has been revolutionised by AlphaFold2, an algorithm that uses neural networks and evolutionary information to predict accurate models from the primary sequence. However, some proteins remain difficult to predict. Moreover, proteins are dynamic entities that e...
ORGANISM(S): Escherichia Coli 
2023-02-22 | PXD036833 | JPOST Repository
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 
ProteomicsReliable identification of protein-protein interactions by crosslinking mass spectrometry_AP-MS
Quantitative proteomics dataset on soluble, affinity-enriched proteins from SPA-pulldowns in E. coli K12, on rpoB-SPA / nusG-SPA / yacL-SPA. This data was used to identify proteins for enrichment analysis and subsequent crosslinking mass spectrometry search (DB creation). Cleared E. coli lysate was ...
ORGANISM(S): Escherichia Coli 
2021-04-14 | PXD024146 | JPOST Repository
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