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ProteomicsOn the reproducibility of label-free quantitative cross-linking/mass spectrometry
Quantitative cross-linking/mass spectrometry (QCLMS) is an emerging approach to study conformational changes of proteins and multi-subunit complexes. Distinguishing protein conformations requires reproducibly identifying and quantifying cross-linked peptides. Here we analyzed the variation between m...
ORGANISM(S): Homo sapiens (Human) 
2018-01-02 | PXD007250 | Pride
Cross-linking Mass-spectrometry Skyline Quatitation 
ProteomicsA model dataset for quantitative cross-linking/mass spectrometry using isotope-labeled cross-linkers
Dynamic proteins and multi-protein complexes govern most biological processes. Cross-linking/mass spectrometry (CLMS) is increasingly successful in providing residue-resolution data on static proteinaceous structures. In order to investigate the technical feasibility of recording dynamic processes u...
ORGANISM(S): Homo sapiens (Human) 
2016-05-06 | PXD004107 | Pride
Model dataset Isotope-labeled cross-linkers Hsa Quantitative cross-linking/mass spectromentry 
ProteomicsQuantitative cross-linking/mass spectrometry
Dynamic proteins and multi-protein complexes govern most biological processes. Cross-linking/mass spectrometry (CLMS) is increasingly successful in providing residue- resolution data on static proteinaceous structures. Here we investigate the technical feasibility of recording dynamic processes usin...
ORGANISM(S): Homo sapiens (Human) 
2015-06-08 | PXD002142 | Pride
Protein dynamics Structual biology Quantitation Cross-linking 
ProteomicsData independent acquisition cross-linking/mass spectrometry
Quantitative cross-linking/mass spectrometry (QCLMS) provides increasing structural detail on altered protein states in solution. Accurate quantitation is a value in itself but may also be central to elucidating small differences between protein states. Hence, QCLMS could benefit from data independe...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) Oryctolagus cuniculus (Rabbit) Gallus gallus (Chicken) Equus caballus (Horse) 
2019-01-25 | PXD011036 | Pride
Xi Reproducibility Spectronaut Data independent acquisition Label-free Mass spectrometry Quantitation Cross-linking 
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 
ProteomicsStructural analysis of substrate-bound ATP-independent proteasomal activator Bpa from Mycobacterium tuberculosis
Chemical cross-linking coupled to mass spectrometry using the amine-reactive BS3 reagent was used to study the interaction between the bacterial proteasome inhibitor, Bpa, and its substrate protein, heat shock repressor HspR.
ORGANISM(S): Mycobacterium tuberculosis H37Rv 
2025-03-17 | PXD047368 | Pride
Chemical cross-linking  bs3  structural proteomics  bacterial proteasome activator 
ProteomicsStoichiometric and structural analyses support the 48:12 model of the human pyruvate dehydrogenase complex core
Chemical cross-linking coupled to mass spectrometry using the amine-reactive BS3 reagent was used to study the organization of the human pyruvate dehydrogenase complex core consisting of multiple copies of dihydrolipoamide acetyltransferase (E2) and dihydrolipoamide dehydrogenase-binding protein (E3...
ORGANISM(S): Homo sapiens (Human) 
2024-05-15 | PXD045858 | Pride
Chemical cross-linking  bs3  structural proteomics  pyruvate dehydrogenase 
ProteomicsCross-linking mass spectrometry of yeast mitochondria grown on different carbon sources reveal Ndi1, Min8 and Pet9 associated with the electron transport chain
Mitochondria derived from Saccharomyces cerevisiae grown on either a non-fermentable (glycerol) or a fermentable (glucose) carbon source were cross-linked with BS3. Additionally, by using a stable-isotope labelled quantitative cross-linking approach, we were able to quantify differences in protein-p...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2020-04-27 | PXD017620 | Pride
Carbon source Cross-linking Mass spectrometry Quantitative Yeast Saccharomyces cerevisiae Qxl-ms Xl-ms Mitochondria 
ProteomicsCross-linking/mass spectrometry analysis of AUGMIN complex
We applied cross-linking/mass spectrometry to characterize in vivo Augmin from Drosophila in absence of any other structural information. The identified cross-links revealed topology of the Augmin complex and allowed us to predict potential interfaces between Augmin and γ-TuRC.
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2017-04-04 | PXD006246 | Pride
Augmin complex Cross-linking/mass spectromentry 
ProteomicsStructural analysis of the native TREX complex from S. cerevisiae
Chemical cross-linking coupled to mass spectrometry was used to study the endogenously purified S. cerevisiae TREX complex. Cross-linking was performed using (a) bis(sulfosuccinimidyl) suberate (BS3) or (b) a combination of adipic dihydrazide (ADH) and 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmo...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2023-09-15 | PXD025843 | Pride
Chemical cross-linking  bs3  adh  dmtmm  structural proteomics  protein complex  trex complex Tho complex 
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