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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 
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 
ProteomicsAnalysis of bilirubin-induced bovine serum albumin stability using protein denaturation and quantitative cross-linking mass spectrometry
We report the combination of protein-denaturation stability principles with quantitative cross-linking mass spectrometry using isobaric quantitative protein interaction reporter technologies. This method enables the evaluation of ligand-induced protein engagement through analysis of cross-link rela...
ORGANISM(S): Bos taurus (Bovine) 
2024-07-03 | PXD036649 | Pride
Quantitative cross-linking Protein stability Mass spectrometry 
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 
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 
ProteomicsOptimized cross-linking mass spectrometry for in situ interaction proteomics
ecent development of mass spectrometer cleavable protein cross-linkers and algorithms for their spectral identification now permits large-scale cross-linking mass spectrometry (XL-MS). Here, we optimized the use of cleavable disuccinimidyl sulfoxide (DSSO) cross-linker for labeling native protein co...
ORGANISM(S): Homo sapiens (Human) 
2019-04-03 | PXD010796 | Pride
Human Cross-linking mass spectrometry Chromatin 
Proteomicscross-linking mass spectrometry of synaptosome
Cross-linking mass spectrometry data of synaptosome and microsome fractions of mouse cerebellum and hippocampus.
ORGANISM(S): Mus musculus (Mouse) 
2020-12-03 | PXD010317 | Pride
Synaptosome Microsome Cross-linking mass spectrometry 
Proteomicsmitochondria cross-linking mass spectrometry
We performed cross-linking mass spectrometry experiments on intact mitochondria isolated from mouse heart in two conditions, native-state and high-salt treatment to disrupt electrostatic interactions. Both conditions were provided in biological replicates.
ORGANISM(S): Mus musculus (Mouse) 
2017-12-11 | PXD006816 | Pride
Mouse Heart Cross-linking mass spectrometry Mitochondria 
ProteomicsA simplified in vivo cross-linking mass spectrometry strategy for proteome-wide studies.
Chemical cross-linking (XL) coupled to mass spectrometry (MS) has become a powerful approach to probe the structure of protein assemblies. Although most of the applications concerned purified complexes, latest developments focus on large-scale in vivo studies. Pushing in this direction, we describe ...
ORGANISM(S): Neisseria meningitidis Bacteria 
2021-02-25 | PXD021553 | Pride
Click-chemistry Mass spectrometry Structural biology In vivo biochemistry Cross-linking 
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