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ProteomicsSugarQuant: a streamlined pipeline for multiplexed quantitative site-specific N-glycoproteomics
Site-specific regulation of protein N-glycosylation is essential in human cells. However, accurate quantification of glycosylation sites and their individual glycan moieties in a cell-wide manner is still technically challenging. Here, we introduce SugarQuant, an integrated mass spectrometry-based p...
ORGANISM(S): Homo sapiens (Human) 
2020-08-24 | PXD018349 | Pride
Glycosylation 
ProteomicsHYpro16: A Two-Proteome Mixture to Assess Interference in Isobaric Tag-Based Sample Multiplexing Experiments
Isobaric tagging is a powerful strategy for global proteome profiling. A caveat of isobaric tag-based quantification is “interference” which may be caused by co-eluting peptides that are co-isolated, co-fragmented, and co-analyzed, thereby confounding quantitative accuracy. Here, we present a two-pr...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2021-08-16 | PXD020815 | Pride
Multiplex Tmt Sps-ms3 Standard Lumos Multi-notch 
ProteomicsStatistical models for the analysis of isobaric Tags multiplexed quantitative proteomics
ABSTRACT: Mass spectrometry is being used to identify protein biomarkers that can facilitate development of drug treatment. Mass spectrometry based proteomics results in complex proteomic data that is hierarchical in nature often with small sample size studies. Generalized linear models (GLM) is th...
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2017-07-28 | PXD005486 | Pride
Statistical models : proteomics Tmt Mixed models Biomarkers 
UnknownA streamlined pipeline for multiplexed quantitative site-specific N-glycoproteomics.
Not available
S-EPMC7572468 | biostudies-literature
ProteomicsDNA-PKcs kinase activity stabilizes the transcription factor Egr1 in activated immune cells
To gain insight into the function of DNA-PKcs within immune cells, we performed a quantitative phosphoproteomic screen in T cells to identify first order phosphorylation targets of DNA-PKcs. Results indicate that DNA-PKcs phosphorylates the transcription factor Egr1 (early growth response protein 1)...
ORGANISM(S): Homo sapiens (Human) 
2021-12-21 | PXD026352 | Pride
Ms3 Phospo Tmt 
ProteomicsUSP28 enables oncogenic transformation of respiratory cells and its inhibition potentiates molecular therapy targeting mutant EGFR, BRAF and PI3K.
Oncogenic transformation of lung epithelial cells is a multi-step process, frequently starting with the inactivation of tumor suppressors and subsequent activating mutations in proto-oncogenes, such as members of the PI3K or MAPK family. Cells undergoing transformation have to adjust to changes, suc...
ORGANISM(S): Homo sapiens (Human) 
2022-04-08 | PXD032810 | Pride
Braf Buparlisib C-jun Vemurafenib Usp28 Lung cancer Egfr Pik3ca C-myc Hras gefitinib 
ProteomicsNicotine-induced protein expression profiling reveals mutually altered proteins across four human cell lines
Mass spectrometry-based proteomic strategies can profile the expression level of proteins in response to external stimuli. Nicotine affects diverse cellular pathways, however, the nicotine-induced alterations on the global proteome across human cell lines have not been fully elucidated. We measured ...
ORGANISM(S): Homo sapiens (Human) 
2018-10-26 | PXD005361 | Pride
Pancreas Sps-ms3 Tmt Nicotine Orbitrap fusion 
ProteomicsInhibition of growth factor signaling prevents SARS-CoV-2 replication
Caco-2 cells were mock-infected or infected with SARS-CoV-2 patient isolates (in biological quintruplicates) for one hour, washed, and incubated for 24 hours before cell harvest. Extracted proteins were digested and split to 1) carry out whole-cell proteomics of a tandem mass tag (TMT) 10-plex sampl...
ORGANISM(S): Homo sapiens (Human) 
2020-05-15 | PXD018357 | Pride
Infection Sars-cov-2 Phospho Tmt Covid-19 
ProteomicsBiomechanical rigidity and quantitative proteomics analyses of segmental regions of the ocular trabecular meshwork at physiologic and elevated pressures
The extracellular matrix (ECM) of the ocular trabecular meshwork (TM) builds resistance to aqueous humor outflow, thereby regulating intraocular pressure (IOP). Glaucoma, a leading cause of blindness worldwide, is associated with changes in the ECM of the TM. The elastic modulus indicates glaucomato...
ORGANISM(S): Homo sapiens (Human) 
2018-01-22 | PXD006424 | Pride
Glaucoma Biomechanical rigidity High resolution mass spectrometry Multi-notch isolation Extended multiplexing Trabecular mesh Quantitative proteomics Human Tandem mass tags 
ProteomicsDecapping activators Edc3 and Scd6 act redundantly with Dhh1 in nutrient-replete cells to post-transcriptionally repress starvation-induced pathways
Degradation of many yeast mRNAs involves decapping by Dcp1:Dcp2. Previous studies on decapping activators Edc3 and Scd6 suggested limited roles in promoting mRNA decay in yeast cells. RNA-seq analysis of mutants lacking one or both proteins reveals that Scd6 and Edc3 have largely redundant functions...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2025-10-30 | PXD053307 | Pride
Mrna decay Yeast Translation 
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