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ProteomicsMS analysis of SARS-CoV2 proteins from patient samples
We developed a simple, MS-based method to specifically detect SARS-CoV-2 proteins from gargle solution samples of COVID-19 patients. Our protocol consists of an acetone precipitation and tryptic digestion of proteins contained within the gargle solution, followed by a targeted MS analysis. Our metho...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2020-07-16 | MSV000085761 | MassIVE
ProteomicsEnsured auxin sensing by degron flexibility
Using a structural proteomics approach via chemical cross-linking combined with mass spectrometry (XL-MS), we have resolved SCFTIR auxin·AUX/IAA complex overall topology, and established the power of IDRs modulating auxin receptor assemblies.
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2020-05-11 | PXD015285 | Pride
Auxin Cross-linking Iaa12 Auxin receptor Xl-ms Idrs Indole-3-acetic acid Aux/iaas Iaa7 Scf-type e3 ubiquitin ligase Tir1 
ProteomicsFirst direct observation of elongated conformational states in alpha-synuclein upon liquid-liquid phase separation
α-Synuclein (α-syn) is an intrinsically disordered protein (IDP) that undergoes liquid-liquid phase separation (LLPS), fibrillation, and forms insoluble intracellular Lewy’s bodies in neurons, which are the hallmark of Parkinson’s Disease (PD). Neurotoxicity precedes the formation of aggregates and ...
ORGANISM(S): Homo sapiens (Human) 
2024-03-18 | PXD033205 | Pride
Cross-linking mass spectrometry liquid-liquid phase separation alpha-synuclein 
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 
ProteomicsCross-linking/Mass Spectrometry Combined with Ion Mobility on a timsTOF Pro Instrument for Structural Proteomics
The combination of cross-linking/mass spectrometry (XL-MS) and ion mobility is still underexplored for conducting protein conformational and protein-protein interaction studies. We present a method for analyzing cross-linking mixtures on a timsTOF Pro mass spectrometer that allows separating ions ba...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) Escherichia coli 
2022-03-17 | PXD027234 | Pride
Ion mobility Mass spectrometry Chemical cross-linking Protein 3d-structure Protein interaction networks 
ProteomicsCombining Affinity Enrichment, Cross-Linking with Photo-Amino Acids, and Mass Spectrometry for Probing Protein Kinase D2 Interactions
We present an approach that relies on the affinity enrichment of a target protein from a complex mixture, followed by a UV-induced activation of incorporated diazirine photo-reactive amino acids (photo-methionine and photo-leucine) and a covalent fixation of interaction partners. The captured protei...
ORGANISM(S): Homo sapiens (Human) 
2017-04-10 | PXD005349 | Pride
Pkd2 Affinity enrichment Protein interaction Photo-cross-linking Photo-methionine Photo-leucine Orbitrap fusion 
ProteomicsProteome analysis of subcellular fractions of HeLa cells
We investigated the interaction network of human PKD2 in the cytosol as well as in Golgi-enriched subcellular protein fractions, using an affinity enrichment strategy combined with chemical cross-linking/mass spectrometry (MS). Analysis of the subproteomes revealed the presence of distinct proteins ...
ORGANISM(S): Homo sapiens (Human) 
2016-09-27 | PXD003917 | Pride
Human Hela cells Subcellular fractionation Proteome analysis Orbitrap fusion 
ProteomicsIdentification of human PKD2 interaction partners from cytosolic protein fractions of HeLa cells by affinity enrichment cross-linking/MS
We investigated the interaction network of human PKD2 in the cytosol as well as in Golgi-enriched subcellular protein fractions, using an affinity enrichment strategy combined with chemical cross-linking/mass spectrometry (MS). Analysis of the subproteomes revealed the presence of distinct proteins ...
ORGANISM(S): Homo sapiens (Human) 
2016-09-27 | PXD003909 | Pride
Human Pkd2 Cross-linking/ms Affinity enrichment Orbitrap fusion 
ProteomicsIdentification of human PKD2 interaction partners from Golgi-enriched protein fractions of HeLa cells by affinity enrichment cross-linking/MS
We investigated the interaction network of human PKD2 in the cytosol as well as in Golgi-enriched subcellular protein fractions, using an affinity enrichment strategy combined with chemical cross-linking/mass spectrometry (MS). Analysis of the subproteomes revealed the presence of distinct proteins ...
ORGANISM(S): Homo sapiens (Human) 
2016-09-27 | PXD003913 | Pride
Human Pkd2 Hela cells Cross-linking/ms Affinity enrichment Golgi apparatus Orbitrap fusion 
ProteomicsExploring GPCR-arrestin interfaces with genetically encoded crosslinkers
-arrestins (arr1 and arr2) are ubiquitous regulators of G protein-coupled receptor (GPCR) signalling. Available data suggest that -arrestins dock to different receptors in different ways. However, the structural characterization of arrestin-GPCR complexes is challenging and alternative approaches to...
ORGANISM(S): Homo sapiens (Human) 
2020-09-21 | PXD020418 | Pride
-arrestins / genetically encoded crosslinkers / g protein-coupled receptor / gpcr-arrestin complexes / live cells 
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