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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 
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 
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 
ProteomicscapsPASEF – Collisional Cross Section Assisted Precursor Selection Applied to Cross-linking Mass Spectrometry
Ion mobility separates molecules in the gas-phase on their physico-chemical properties, providing information about their size as collisional cross-sections. The timsTOF Pro combines trapped ion mobility with a quadrupole, HCD cell and a time-of-flight mass spectrometer, to interrogate ions at high ...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) 
2020-07-22 | PXD018189 | Pride
Ion mobility Cross-linking mass spectrometry Xl-ms Phox 
ProteomicsDon’t Waste Time – Ensure Success in Your Cross-Linking Mass Spectrometry Experiments Before You Begin.
Cross-linking mass spectrometry (XL-MS) is becoming a more popular tool for researchers to turn towards for studying proteins and their complexes of interest especially in complex samples such as lysates or whole-cells. Studying a targeted proteins in a complex mixture can be difficult as data on ot...
ORGANISM(S): Neisseria meningitidis serogroup C (strain 8013) Bacteria 
2024-02-07 | PXD045792 | Pride
Cross-linking Mass spectrometry Protein abundance Ibaq 
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 
ProteomicsA Simple Cross-Linking/Mass Spectrometry Workflow to Study System-Wide Protein Interactions in Drosophila Embryos
We provide a cross-linking/MS workflow that can be applied to complex systems. The software tool MeroX 2.0 can be used to identify cross-linked peptide on a proteome-wide level. We applied the workflow to extracts of Drosophila embryos and identified 5,129 unique cross-linked residue pairs in biolog...
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2019-07-09 | PXD012546 | Pride
Cross-linking Mass spectrometry Xlms Cxms Drosophila 
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 
ProteomicsQuantitative cross-linking/mass spectrometry reveals subtle protein conformational changes
We have developed quantitative cross-linking/mass spectrometry (QCLMS) to interrogate conformational rearrangements of proteins in solution. Our workflow was tested using a structurally well-described reference system, the human complement protein C3 and its activated cleavage product C3b. We found ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2016-06-16 | MSV000079827 | MassIVE
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