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ProteomicsLFQ proteomics analysis of M. smegmatis treated with BacPROTACs.
To monitor selective degradation of ClpC1 and ClpC2 using BacPROTAC compounds in M. smegmatis we performed a LFQ proteomics analysis treating the cells at bactericidal compound concentration. We detected degradation of both proteins and additional dysregulation of the mycobacterial PQC system.
ORGANISM(S): Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) 
2023-06-07 | PXD037235 | Pride
Antibiotics Tpd Bacprotac Protac Protein degradation 
ProteomicsLFQ proteomics analysis of the M. smegmatis ClpC2 interactome.
To assess the ClpC2 interactome, a IP-MS analysis was performed using ectopically expressed tagged ClpC2 in a ClpC2 deficient cell line. To evaluate potential binding sites on ClpC2, CymA treatment was applied to compete with potential interactors for a shared ClpC2 binding site.
ORGANISM(S): Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) 
2023-06-07 | PXD037231 | Pride
Antibiotics Tpd Protein degradation 
ProteomicsA quantitative proteomics approach to monitor targeted protein degradation in M. smegmatis
Targeted protein degradation via the ubiquitin proteasome has been established in eukaryotes, however no application has been shown in bacteria so far. In the present work, selective protein degradation is shown using hetero bifunctional drugs, bringing substrates in close proximity to the bacterial...
ORGANISM(S): Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) Bacteria 
2022-08-12 | PXD021505 | Pride
Mycobacteria Targeted protein degradation Protease Tpd 
ProteomicsLFQ proteomics analysis of M. smegmatis treated with CymA and ecumicin (Part 1).
To assess the impact of the bactericidal compounds CymA and ecumicin on the mycobacterial proteome and to monitor proteome remodeling by the AAA+ ClpC1 protease machinery, we performed a LFQ proteomics analysis treating the cells at sub-bactericidal compound concentration. We identified new players ...
ORGANISM(S): Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) 
2023-06-07 | PXD037232 | Pride
Tuberculosis Tpd Protein degradation 
ProteomicsLFQ proteomics analysis of M. smegmatis treated with CymA and ecumicin (Part 2).
To assess the impact of the bactericidal compounds CymA and ecumicin on the mycobacterial proteome and to monitor proteome remodeling by the AAA+ ClpC1 protease machinery, we performed a LFQ proteomics analysis treating the cells at bactericidal compound concentration. We identified new players of t...
ORGANISM(S): Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) 
2023-06-07 | PXD037234 | Pride
Antibiotics Tuberculosis Tpd Protein degradation 
ProteomicsComparative analysis of MS sample preparation methods
We compare the most commonly used proteomic sample preparation strategies such as classical in solution digest protocols, SPEED, FASP, STrap, SP3, as well as the commercially available kits iST (PreOmics) and EasyPep (Thermo Scientific) in their efficacy to extract proteomes from HeLa cells. We find...
ORGANISM(S): Homo sapiens (Human) 
2022-09-06 | PXD030406 | Pride
Hela Human Sample preparation Lc-ms/ms 
ProteomicsA causal model of ion interference enables assessment and correction of ratio compression in multiplex proteomics
We thoroughly characterize isobaric labeling (TMT)-associated reporter ion interference at the MS2 level using a defined two-proteome experimental system with known ground truth. We discover remarkably poor agreement between the apparent precursor purity in the isolation window and the actual level ...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae Saccharomyces cerevisiae (Baker's yeast) 
2023-12-19 | PXD040449 | Pride
Ion interference Tmt Ratio compression Isobaric label 
ProteomicsDeletion of GSE1 and HDAC1 inactivation alters proteomic profiles and cell cycle control
The DNA damage response (DDR) is orchestrated by multiple, tightly regulated signalling events. We discovered that genetic suppressor element 1 (GSE1) forms a complex with the histone deacetylation 1 (HDAC1) / CoREST complex and that loss of GSE1 hampers DDR induction. To investigate how GSE1 and HD...
ORGANISM(S): Homo sapiens (Human) 
2023-10-23 | PXD040339 | Pride
Acetylome Hdac1 Gse1 Phosphorylome Hap1 Dna damage response 
ProteomicsRegulation of cellular proteome and acetylome by catalytic and non-catalytic functions of class I histone deacetylases
Project description: Taking advantage of a newly generated model system, we examined the influence of class I HDAC catalytic and non-catalytic function on the cellular proteome and acetylome. Therefore, we generated HAP1 cell lines either lacking individual class I HDACs or expressing catalytically ...
ORGANISM(S): Homo sapiens (Human) 
2022-08-16 | PXD030164 | Pride
Acetylome Chromatin Hdac inhibitor Histone deacetylase 
ProteomicsCellular concentrations of Protein Kinase D1 in HEK293T and INS-1 cells
Protein kinase D1 (PRKD1, also referred to as PKD1), has been proposed to undergo concentration dependent dimerization in vitro. To test whether the cellular concentration of PKD1 is in the range of the dissociation constant obtained, the expression level of PKD1 was investigated by PRM. To this end...
ORGANISM(S): Homo sapiens (Human) Rattus norvegicus (Rat) 
2019-08-19 | PXD013232 | Pride
Pkd1 Ins-1 Protein kinase d Hek293t 
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