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ProteomicsArabidopsis thaliana responds to colonisation of Piriformospora indica by secretion of symbiosis specific proteins
Plants interact with a wide variety of fungi in a mutualistic, parasitic or neutral way. The associations formed depend on the exchange of nutrients and signalling molecules between the partners. The latter include a diverse set of protein classes, of which some have been demonstrated to be functiona...
ORGANISM(S): Piriformospora Sp. Arabidopsis Thaliana (mouse-ear Cress) 
2019-01-07 | PXD009563 | Pride
Scopolin Er body Piriformospora indica Plat Secretome 
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ProteomicsA rendezvous of two second messengers: The c-di-AMP receptor protein DarB controls (p)ppGpp synthesis in Bacillus subtilis
DarB is a cyclic di-AMP binding protein consisting of two CBS (Cystathionine-beta synthase) domains. To reveal the global role of the second-messenger, understanding the function of the receptor proteins is fundamental. In order to do so, we aimed to identify potential binding partners of DarB in vit...
ORGANISM(S): Bacillus Subtilis Subsp. Subtilis Str. 168 
2021-01-12 | PXD018087 | Pride
Second messengers Bacillus subtilis C-di-amp receptor Pull-down Darb Rela 
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ProteomicsStructural basis for the c-di-AMP - dependent regulation of the stringent response by DarB
The bacterial second messenger c-di-AMP controls various cellular processes including potassium and osmolyte homeostasis. The c-di-AMP receptor protein DarB of Bacillus subtilis binds to the Rel protein and triggers the Rel-dependent stringent response. Here we report crystal structures of DarB in th...
ORGANISM(S): Bacillus Subtilis Subsp. Subtilis 
2022-08-12 | PXD033346 | Pride
Bs3 Cx-ms Darb 
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ProteomicsFishing for SAM/SAH-binding proteins
The aim of the project was to identify S-adenodsyl methionine-binding proteins expressed in D. melanogaster S2 cells. For this puprose a capture compund reagent carrying a SAH-affinity group, a biotin group for enrichment and a cross-linking moiety consisting of either benzophenone or a nitrobenzene...
ORGANISM(S): Drosophila Melanogaster (fruit Fly) 
2019-02-25 | PXD006245 | Pride
Lysine methylation S-adenosyl-methionine Methyltransferase Capture compound 
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ProteomicsProteome analysis of Jurkat cells for spectral library
In order to increase the spectral library to study the ocurrence of distinct peptide fragmetation patterns, we analyzed the whole cell proteome of Jurkat cells.
ORGANISM(S): Homo Sapiens (human) 
2019-02-25 | PXD005111 | Pride
Whole cell lysate Spectral library Fragmentation pattern 
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ProteomicsIdentification of human membrane proteins
Typically, integral membrane and membrane associate proteins are underrepresented in proteomic experiments due to their low abundance and solubility during sample preparation. We collected two fractions upon cell lysis, one comprising the insoluble membrane fraction the other the soluble cytosolic fr...
ORGANISM(S): Homo Sapiens (human) 
2019-02-25 | PXD005063 | Pride
Quantitatie proteomics Membrane proteins 
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ProteomicsProtein expression difference in Drosophila speciation
We aim to determine the difference of protein expression in the closely related Drosophila species D.melanogaster and D.simulans to gain further insight into protein expression profiles of both species. Analysis of the protein levels might hint to pathways that have evolved into different direction a...
ORGANISM(S): Drosophila Melanogaster (fruit Fly) 
2019-02-25 | PXD005060 | Pride
Quantitative proteomics Shotgun proteomics Novel slice variants Drosophila speciation 
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ProteomicsStability of peptide fragmentation patterns
Our study aims to determine the stability of fragmetnation patterns of peptides upon collision-induced dissociation (CID). Recent studies reported that for a minority of peptides, CID fragmentation leads to non-reproducible fragmentation spectra and therefore impaired identification. In order to stud...
ORGANISM(S): Homo Sapiens (human) 
2019-02-25 | PXD006691 | Pride
Peptide fragmentation Peptide identification Tandem ms Collision-induced dissociation 
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ProteomicsDREX proteome analysis for spectral library
In order to prepare a spectral library for data-indepentend acquisition mass spectrometry studies, we try to cover as many proteins from Drosophila melanogaster embryonic protein extracts.
ORGANISM(S): Drosophila Melanogaster (fruit Fly) 
2019-02-25 | PXD005100 | Pride
Drosophila embryo proteome Spectral library Fragmentation pattern 
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TranscriptomicsExpression data of Myh6-MeCP2 transgenic mice
Hearts of Myh6-MeCP2 transgenic mice and wildtype littermates were rapidly dissected and flash frozen. We used Affymetrix microarrays to assess gene expression changes induced by overexpression of MeCP2 under the control of a cardiomycyte specific promoter. Hearts were dissected 2-3 weeks after birth...
ORGANISM(S): Mus musculus 
2015-12-22 | E-GEOD-52797 | biostudies-arrayexpress
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