Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Differential Enzymatic 16O/18O Labelling for the Detection of Cross-Linked Nucleic Acid-Protein Heteroconjugates

ABSTRACT: Enzymatic differential 16O/18O labelling of nucelic acid-protein heteroconjugates. Heteroconjugates are identified against a complex background using an automated analysis workflow.

INSTRUMENT(S): Bruker Daltonics solarix series

ORGANISM(S): Bos Taurus (bovine)

SUBMITTER: Timo Sachsenberg

LAB HEAD: Oliver Kohlbacher

PROVIDER: PXD003673 | Pride | 2017-09-11

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	BSA_a.mzML	Mzml
	BSA_b.mzML	Mzml
	BSA_c.mzML	Mzml
	HetsBCDBSA1_1a-tiox.mzML	Mzml
	HetsBCDBSA1_1a.mzML	Mzml

Items per page:

1 - 5 of 15

Publications

Differential Enzymatic 16O/18O Labeling for the Detection of Cross-Linked Nucleic Acid-Protein Heteroconjugates.

Flett Fiona J FJ Sachsenberg Timo T Kohlbacher Oliver O Mackay C Logan CL Interthal Heidrun H

Analytical chemistry 20171013 21

Cross-linking of nucleic acids to proteins in combination with mass spectrometry permits the precise identification of interacting residues between nucleic acid-protein complexes. However, the mass spectrometric identification and characterization of cross-linked nucleic acid-protein heteroconjugates within a complex sample is challenging. Here we establish a novel enzymatic differential 16O/18O-labeling approach, which uniquely labels heteroconjugates. We have developed an ...[more]

PMID: 28885003

Similar Datasets

Identification of PM-localized proteins

Project description:In order to assess the quality of alleged PM identifications from Arabidopsis, PM-enriched fractions were compared to PM-depleted fractions using 18O isotopic labeling and mass spectrometry. The two samples submitted are biological replicates. Keywords: Protein Localization via MS Two biological replicates were analyzed in order to assess sample complexity. PM-derived vesicles were digested in 18O water and compared to PM-depleted fractions digested in 16O (natural abundance) water. Relative ion intensities were then used to calculate a heavy/lite ratio with proteins showing enrichment in the upper phase having a ratio greater than 1 or 0 on a log2 scale.

2005-06-21 | E-GEOD-2830 | biostudies-arrayexpress

AP-MS of helicase Upf1 in PC12 cells

Project description:DNA/RNA helicase Upf1 seems to interact with axonal transcripts in response to nerve growth factor (NGF, A. Ludanyi, M. Gaspari and A. Riccio, unpublished data). In order to shed light on Upf1 mechanism of action and to identify potential associations with molecules having cleavage activity, we performed an AP-MS experiment comprising Upf1 immunoprecipitation, on-beads digestion, isotopic labelling (18O) and quantitative LC-MS/MS analysis.

2021-09-10 | PXD023586 | Pride

CD4+ Th immunogenicity of Ascaris spp.

Project description:Application of a reconstituted in vitro system to define the CD4+ Th immunogenicity of complex antigenic mixtures.

2020-03-04 | PXD015924 | Pride

Quantitative analysis of in vivo methionine oxidation of the human proteome

Project description:A novel stable isotope labelling stategy was developed to quantify methionine oxidation in an unstressed human proteome. Cell extracts were oxidized with 18O labelled hydrogen peroxide following cell lysis in order to convert all unoxidized methionine residues to an oxidized version with a heavy label. The heavy labelled peptides were used to generate a custom search and quantification of the relative ratios between heavy and light labelled methionine sulfoxide containing peptides. Where the light labelled peptides were in vivo oxidized

2019-07-26 | PXD014770 | Pride

Quantitative analysis of in vivo methionine oxidation of the human proteome

Project description:A novel stable isotope labelling strategy was developed to quantify methionine oxidation in an unstressed human proteome. Cell extracts were oxidized with 18O labelled hydrogen peroxide following cell lysis in order to convert all unoxidized methionine residues to an oxidized version with a heavy label. The heavy labelled peptides were used to generate a custom search and quantification of the relative ratios between heavy and light labelled methionine sulfoxide containing peptides. Where the light labelled peptides were in vivo oxidized

2019-12-09 | PXD014629 | Pride

Dynamic metabolic reprogramming in dendritic cells: an early response to influenza infection that is essential for effector function

Project description:In response to influenza infection we found that dendritic cells (DCs), cells that are critical in mounting an effective immune response, undergo a profound metabolic shift. DCs alter the concentration and location of hundreds of proteins, including c-MYC, mediating a shift to a highly glycolytic phenotype that is also flexible in terms of fueling respiration.

2021-09-08 | PXD013690 | Pride

Peroxynitrite-mediated post-translational modification of human glutamine synthetase

Project description:The aim of the project was to understand the mechanisms that underlie the oxidative inactivation of human glutamine synthetase (HsGS). For that purpose, we expressed and purified recombinant HsGS, exposed it in phosphate buffer to peroxynitrite (ONOO-) and assessed the functional and structural consequences. To characterize the oxidative post-translational modifications induced by ONOO-, several approaches were carried out (e.g. SDS-PAGE, western-blot, amino acid quantification by LC, etc). The most detailed characterization was performed through LC-MS/MS analysis after trypsin digestion of the ONOO--treated protein, which allowed us to identify the amino acid residues that are modified and to estimate the extent of such modifications.

2023-05-10 | PXD037583 | Pride

Proteomics of Alzheimer's Disease mouse models

Project description:Alzheimer’s disease (AD) is a neurodegenerative disease displaying plaques formed by the neurotoxic amyloid β-peptide (Aβ) and intracellular neurofibrillary tangles consisting of protein tau. However, how these pathologies relates to the massive neuronal death that occurs in AD brains remain elusive. To identify proteins, the levels of which are affected by increased Aβ levels, we performed a proteomic analysis of the AD mouse model APPsw and compared it to that of APPsw mice lacking the major Aβ degrading enzyme neprilysin. This was achieved by establishing an LC-MS/MS method to analyze brain homogenate, using an 18O-labeled internal standard to accurately quantify the protein levels. By this approach we identified approximately 600 proteins and could quantify the levels of 300 of these. Interestingly, several proteins, including some not previously reported to be associated with AD, were identified. The relevance of these proteins for AD warrants further research.

2015-07-29 | PXD000968 | Pride

Proteomics of Alzheimer's Disease mouse models - control dataset

Project description:Alzheimer’s disease (AD) is a neurodegenerative disease displaying plaques formed by the neurotoxic amyloid β-peptide (Aβ), and intracellular neurofibrillary tangles consisting of protein tau. However, how these pathologies relates to the massive neuronal death that occurs in AD brains remain elusive. Neprilysin is the major A degrading enzyme and a lack thereof increases A levels in the brain twofold. To identify altered protein expression levels induced by increased Aβ levels, we performed a proteomic analysis of the brain of the AD mouse model APPsw and compared it to that of APPsw mice lacking neprilysin. To this end we established an LC-MS/MS method to analyze brain homogenate, using an 18O-labeled internal standard to accurately quantify the protein levels. To distinguish between alterations in protein levels directly caused by increased A levels and those induced by neprilysin deficiency independently of A, the brain proteome of neprilysin deficient APPsw mice was compared to that of neprilysin deficient mice. By this approach we identified approximately 600 proteins and could quantify the levels of 300 of these. Pathway analysis showed that many of the proteins with altered expression were involved in neurological disorders, and that tau, presenilin and APP were key regulators in the identified networks. The data have been deposited to the ProteomeXchange Consortium with identifier PXD000968. Interestingly, the levels of several proteins, including some not previously reported to be associated with AD, were associated with increased A levels.

2015-07-29 | PXD001786 | Pride

Mps1 Phosphorylation of the Molecular Chaperone Hsp90 Regulates Mitotic Checkpoint

Project description:SUMMARY Mps1 protein kinase is required for accurate chromosome segregation during the mitotic checkpoint. The molecular chaperone Heat Shock Protein 90 (Hsp90) has been linked to Mps1 activity, however the molecular mechanismsunderlying this regulatory process remain elusive. We report that Mps1 directly phosphorylates a conserved threonine residue (T101 in yeast Hsp90 and T115 in human Hsp90) in the N domain of Hsp90. This phosphorylation regulates chaperone function by reducingHsp90 ATPase activity andfosteringits association with kinase client proteins including Mps1. Phosphorylation of T101is also essential for the mitotic checkpoint because it confers Mps1 stability and activity.Additionally,Mps1 phosphorylation of Hsp90 sensitizes cells to Hsp90 inhibitors and elevated Mps1 levels confer tumor selectivity on Hsp90 drugs.Finally,we identified Cdc14 as the phosphatasethat dephosphorylatesT101 and disruptsthe Mps1-Hsp90 interaction. This leads to degradation of Mps1,thusproviding a mechanism for its inactivation and mitotic exit.

2016-01-27 | PXD001969 | Pride