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ProteomicsProteolytic processing of CD99
The adhesion molecule CD99 is essential for transendothelial migration (TEM) of leukocytes. Here we demonstrate by biochemical and cellular assays that CD99 undergoes ectodomain shedding by the metalloprotease meprin ? and subsequent intramembrane proteolysis by ?-secretase. The cleavage site in CD9...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-29 | MSV000080746 | MassIVE
ProteomicsThe E3 ubiquitin ligase HectD3 is a novel regulator of cardiac hypertrophy and inflammation
The HECT domain E3 ubiquitin protein ligase 3 (HectD3) is highly expressed in the heart, but its cardiac function is still unknown. Here, we identified SUMO2 and Stat1 as novel cardiac substrates for HectD3. SUMO2 is a potent inducer of Calcineurin-NFAT mediated cardiomyocyte hypertrophy, whereas, S...
ORGANISM(S): Rattus norvegicus (Rat) 
2021-09-09 | PXD020843 | Pride
Ubiquitin ligase Cardiac models Proteomics 
ProteomicsA mitochondrial sirtuin shapes the intestinal microbiota by controlling lysozyme expression
Sirtuins are sensors that orchestrate cellular responses to adapt to changing situations. Here, we show that a protein-restricted diet induces strongly induces increased intestinal expression of the sole Drosophila mitochondrial sirtuin, dSirt4. To elucidate the effects of deregulated dSirt4 express...
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2025-06-23 | PXD054704 | Pride
Drosophila  lc-ms  sirtuin-4 
ProteomicsMiniaturized sample preparation on a digital microfluidics device for sensitive bottom-up microproteomics of mammalian cells using magnetic beads and mass spectrometry-compatible surfactants
We used digital microfluidics (DMF) for the sample preparation of approximately 100 mammalian cells, and subsequent bottom-up proteome analysis by LC-MS. This comprised optimization of cell lysis conditions for DMF, the development of detergent-buffer systems, and adaptation of the single-pot, solid...
ORGANISM(S): Homo sapiens (Human) 
2019-10-07 | PXD014158 | Pride
Digital microfluidics Detergents Sp3 Microproteomics Miniaturization 
ProteomicsProtein aggregation is a consequence of the dormancy-inducing membrane toxin TisB in Escherichia coli
Protein aggregates occur in all living cells due to misfolding of proteins. In bacteria, protein aggregation is associated with cellular inactivity, which is related to dormancy and tolerance to stressful conditions, including the exposure to antibiotics. In Escherichia coli, the membrane toxin TisB...
ORGANISM(S): Escherichia coli 
2024-10-04 | PXD049478 | Pride
Toxin-antitoxin system Antibiotics Dormancy Protein aggregation Type i toxin 
ProteomicsHuman APOE3 expressing mice are more prone to develop fatty liver disease on a high fat and sugar diet compared to APOE4 mice
Recent findings suggest that the human APOE epsilon 4 allele protects against non-alcoholic fatty liver disease, while APOE epsilon 3 promotes hepatic steatosis and steatohepatitis. We performed an untargeted proteome analysis of the liver and identified a great number of proteins differently expres...
ORGANISM(S): Mus musculus (Mouse) 
2024-05-21 | PXD033973 | Pride
Hepatic steatosis Apolipoprotein e polymorphism 2d-lc Dietary restriction Tmt 
ProteomicsThiol reactive tandem mass tags for quantitative top-down proteomics
Here, we describe the development of a labeling strategy for TDP targeting thiol groups of cysteine residues with iodoTMTsixplex. While this method inherently excludes the quantification of cysteine-free proteoforms, it provides the opportunity of sixplexing and the implementation of multidimensiona...
ORGANISM(S): Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2021-08-06 | PXD026310 | Pride
Isobaric labeling Gelfree High ph fractionation Yeast Iodotmtsixplex Quantitative top-down proteomics Saccharomyces cerevisae Escherichia coli 
ProteomicsDifferential proteome analysis of Escherichia coli grown on acetate vs. glucose
Relative protein abundances of Escherichia coli growing exponentially on minimal medium with acetate or glucose as the sole carbon source were investigated in a quantitative shotgun proteome analysis with TMT6-plex isobaric tags. Peptides were separated by high resolution high/low pH 2D-LC, using an...
ORGANISM(S): Escherichia coli 
2016-10-11 | PXD003863 | Pride
Tmt Isobaric High/low ph 2d-lc 
ProteomicsSCX, 18O-labeling and charge reversal for C-terminomics
The proteome wide, mass spectrometry based identification of protein C-termini is hampered by factors such as poor ionization efficiencies, low yields in labeling strategies or the need for enrichment procedures. We present a bottom-up proteomics workflow to identify protein C-termini utilizing a co...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2019-06-20 | PXD013486 | Pride
Lc-ms Charge-reversal derivatization C-terminomics 
ProteomicsInfluence of Different Sample Preparation Approaches on Proteoform Identification by Top-Down Proteomics
Top-down proteomics (TDP) has made significant advances in the past, and a plethora of sample preparation workflows have been developed. Here, we systematically investigated the influence of different sample preparation steps on proteoform and protein identifications, including cell lysis, reduction...
ORGANISM(S): Homo sapiens (Human) 
2024-08-08 | PXD049969 | Pride
Top-down proteomics  proteoforms  sample preparation  fractionation  mass spectrometry. 
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