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ProteomicsDissection of prognostic traits in colorectal cancer using multi-dimensional proteomics
Colorectal cancer (CRC) is the third most commonly diagnosed cancer worldwide and the second leading cause of cancer death globally. The molecular mechanisms underlying CRC have been investigated using different omics technologies including genomics, proteomics, and metabolomics. Resulting molecular...
ORGANISM(S): Homo sapiens (Human) 
2025-03-26 | PXD044246 | Pride
Proteomics Colorectal cancer Phosphoproteomics 
MetabolomicsDissection of two routes to naïve pluripotency using different kinase inhibitors
Embryonic stem cells (ESCs) can be maintained in the naïve state through inhibition of Mek1/2 and Gsk3 (2i). A relevant effect of 2i is the inhibition of Cdk8/19, which are negative regulators of the Mediator complex, responsible for the activity of enhancers. Inhibition of Cdk8/19 (Cdk8/19i) stimul...
2021-02-10 | MTBLS301 | MetaboLights
ProteomicsMASS SPECTROMETRY ROADMAPS TO NAIVE PLURIPOTENCY
Pluripotency can be maintained in the naïve state through manipulation of ERK and WNT signalling (2i), shielding embryonic stem cells (ESCs) from inductive cues. Alternatively, inhibiting CDK8/19 (CDK8/19i), a repressor of the Mediator co-activator complex, directly stimulates super-enhancer activit...
ORGANISM(S): Mus musculus (Mouse) 
2021-02-10 | PXD018694 | Pride
Phosphoproteomics Mouse stem cells Proteomics 
ProteomicsSpatial-proteomics reveals phospho-signaling dynamics at subcellular resolution
Dynamic change in subcellular localization of signaling proteins is a general concept that eukaryotic cells evolved for responding and elicit a coordinated response to stimuli. Mass spectrometry (MS)-based proteomics in combination with subcellular fractionation can provide comprehensive maps of spa...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) 
2021-11-18 | PXD023690 | Pride
Dia Spatio-temporal dynamics Proteomics Phosphoproteomics 
ProteomicsNarrow-window DIA: Ultra-fast quantitative analysis of comprehensive proteomes with high sequencing depth. Evaluation of window width and injection time.
Mass spectrometry (MS)-based proteomics aims to characterize comprehensive proteomes in a fast and reproducible manner. Here, we present an ultra-fast scanning data-independent acquisition (DIA) strategy consisting on 2-Th precursor isolation windows, dissolving the differences between data-dependen...
ORGANISM(S): Homo sapiens (Human) 
2024-02-01 | PXD046285 | Pride
Dia Astral Proteomics 
ProteomicsNarrow-window DIA: Ultra-fast quantitative analysis of comprehensive proteomes with high sequencing depth. Dilution Series and Single Shot Gradient comparison.
Mass spectrometry (MS)-based proteomics aims to characterize comprehensive proteomes in a fast and reproducible manner. Here, we present an ultra-fast scanning data-independent acquisition (DIA) strategy consisting on 2-Th precursor isolation windows, dissolving the differences between data-dependen...
ORGANISM(S): Homo sapiens (Human) 
2024-02-01 | PXD046283 | Pride
Dia Astral Proteomics 
ProteomicsZAKb is a cellular compression sensor that mediates hypertrophic signaling in skeletal muscle
Mechanosensing is required for the senses of touch and hearing, and impacts on cellular processes such as cell differentiation, migration, invasion and tissue homeostasis. Mechanical inputs give rise to p38- and JNK-signaling, which mediates adaptive physiological responses in various tissues. In mu...
ORGANISM(S): Mus musculus (Mouse) 
2022-05-31 | PXD028548 | Pride
Zak Phosphoproteomics Mouse. muscle 
ProteomicsUnraveling the differential mechanisms of revascularization promoted by MSCs & ECFCs from adipose tissue or umbilical cord in a murine model of critical limb-threatening ischemia.
Critical limb threatening ischemia (CLTI), the most severe manifestation of peripheral artery disease, results from the chronic blockade of peripheral vessels, usually induced by atherosclerosis. CLTI patients suffer from high risk of amputation of the lower extremities and elevated mortality rates,...
ORGANISM(S): Mus musculus (Mouse) 
2024-07-25 | PXD046843 | Pride
Mscs Critical limb-threatening ischemia Proteomics Cell therapy Adipose tissue Ecfcs 
ProteomicsON THE ACCURACY, PRECISION AND STATISTICAL SIGNIFICANCE OF COMPRESSED RATIOS IN ISOBARIC LABELLING
Despite the outstanding advantages that isobaric labelling has to offer in quantitative proteomics, its precision and accuracy are undermined by ratio compression, which is consequence of the co-isolation of peptides within a selected isolation window. Here, using the two-proteomes approach we inves...
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2016-08-08 | PXD003640 | Pride
Isobaric labelling Statistics Accuracy Ratio compression Precision 
ProteomicsUrea artifacts interfere with immunopurification of lysine acetylation
Urea-based buffers can induce carbamylation artefacts. Here we report that carbamylation of lysine residues resembles the structure of acetylated lysines (K-ac) and compete during K-ac immunoaffinity purification. We propose an alternative strategy using an ionic detergent which improves significant...
ORGANISM(S): Homo sapiens (Human) 
2017-01-11 | PXD003701 | Pride
Urea Immunopurification Acetyl Acetylation Carbamylation Carbamyl 
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