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ProteomicsWidespread protein histidine phosphorylation in bacteria
For decades, extreme difficulties in analyzing histidine phosphorylation have limited the study of phosphohistidine signaling. Here we report a method revealing widespread and abundant protein histidine phosphorylation in E. coli. Our new approach generated the largest E. coli phosphoproteome datase...
ORGANISM(S): Escherichia Coli 
2017-12-07 | PXD008369 | JPOST Repository
ProteomicsCombining high resolution and exact calibration to boost statistical power: A well-calibrated score function for high-resolution MS2
This project reanalzyes data from 4 other projects. Information about the samples can be found in the following four publications. The four samples used in this study include a ocean metaproteome sample, a human sample, a E. coli sample, and a Plamodium falciparum sample. B. N. Pease, E. L. Huttli...
ORGANISM(S): Homo sapiens (Human) Plasmodium falciparum (isolate 3D7) Escherichia coli 
2018-09-19 | PXD009265 | Pride
E. coli Score function Ocean Human Plasmodium 
ProteomicsPhosphoproteomic analysis of T cell receptor stimulation-induced changes in human primary CD4+CD25- T cells in the absence or presence of regulatory T cells.
Regulatory T cells (Tregs) suppress other immune cells and are indispensable for human health, yet the molecular mechanisms of suppression remain incompletely understood. Tregs can suppress proliferation and cytokine production of CD4+CD25- conventional T cells (Tcons). We previously demonstrated th...
ORGANISM(S): Homo sapiens (Human) 
2017-08-28 | PXD004291 | Pride
Co-cultures Regulatory t cells (tregs) Ti-imac Human cd4+ t cells Phosphoproteomics 
ProteomicsExtending proteome coverage through an on-line 2D SCX-RP ultra-high pressure system
Ultra high pressure liquid chromatography (UHPLC) systems combined with state of the art mass spectrometers have pushed the limit of deep proteome sequencing to new heights making it possible to identify thousands of proteins in a single LC/MS experiment within a few hours. However, the relationship...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-31 | MSV000080845 | MassIVE
ProteomicsDirect comparison of the hinge-cleaving proteases IgdE and BdpK for LC-MS based IgG1 clonal profiling
Human antibodies are heterogeneous molecules, primarily due to clonal sequence variations. Analytical techniques to assess antibody levels quantitatively, like ELISA assays, lack the power to determine abundances at the clonal level. Recently, we introduced an LC-MS-based approach that can distingui...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2023-08-17 | MSV000092676 | MassIVE
ProteomicsDual-Probe Activity-Based Protein Profiling Reveals Site-Specific Binding Dynamics of EGFR-Directed Drugs
Comparative, dose-dependent analysis of interactions between small molecule drugs and their targets, as well as off-targets, in complex proteomes is crucial for selecting optimal drug candidates. The affinity of small molecules for targeted proteins is largely dictated by interactions between amino ...
ORGANISM(S): Homo sapiens (Human) 
2024-10-17 | PXD045864 | Pride
Chemical proteomics  activity-based protein profiling  site-specific  concentration-dependent analysis  dual-probe comparison. 
ProteomicsPhosphoproteomic analysis of T cell receptor stimulation-induced changes in human primary CD4+CD25- T cells in the absence or presence of regulatory T cells.
This is an addition to dataset PXD004291. This data were only used for confirmation of certain phosphopetides. The dataset was not included in inital analysis due to suboptimal sample preparation.
ORGANISM(S): Homo sapiens (Human) 
2017-08-28 | PXD006142 | Pride
T-cells Phosphoproteomics 
ProteomicsTi4+-IMAC label-free quantification
We combine high-resolution mass spectrometry with Ti4+-IMAC phosphopeptide enrichment and label-free quantification to monitor the phosphoproteome of Jurkat T-cells following stimulation by Prostaglandin E2. Jurkat T lymphoma cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine se...
ORGANISM(S): Homo sapiens (Human) 
2014-05-22 | PXD000293 | Pride
Label-free phosphoproteomics 
TranscriptomicsA central role for TFIID in the pluripotent transcription circuitry [PP003]
Pluripotent stem cells can be isolated from early embryos or induced by cell fusion, somatic nuclear transfer, or expression of a selected set of transcription factors. Embryonic stem (ES) cells are characterized by an open chromatin configuration and high transcription levels achieved via autoregul...
ORGANISM(S): Mus musculus 
2013-03-21 | E-GEOD-33645 | biostudies-arrayexpress
TranscriptomicsA central role for TFIID in the pluripotent transcription circuitry [PP002]
Pluripotent stem cells can be isolated from early embryos or induced by cell fusion, somatic nuclear transfer, or expression of a selected set of transcription factors. Embryonic stem (ES) cells are characterized by an open chromatin configuration and high transcription levels achieved via autoregul...
ORGANISM(S): Mus musculus 
2013-03-21 | E-GEOD-33644 | biostudies-arrayexpress
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