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UnknownMSstatsPTM: Statistical Relative Quantification of Posttranslational Modifications in Bottom-Up Mass Spectrometry-Based Proteomics.
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S-EPMC9860394 | biostudies-literature
ProteomicsAcetylomics of Caco-2 cells Differentiating
Looking at the differentiation of Caco-2 cell into an intestinal epithelial model through acetylomics
ORGANISM(S): Homo sapiens (Human) 
2024-05-29 | PXD049087 | Pride
Acetylomics Tmt Caco-2 Differentiation Intestinal model 
ProteomicsGalectin-1 Modulates Cell Adhesions, Caveolae, and Vascular Permeability in Kidney Endothelial Cells - Insights from Phosphoproteomics
Microvascular inflammation and endothelial injury, triggered by interferon-gamma (IFNgamma), are hallmarks of antibody-mediated rejection (ABMR), the leading cause of premature kidney allograft loss. Chronic ABMR exhibits glomerular basement membrane and extracellular matrix (ECM) remodeling and end...
ORGANISM(S): Homo sapiens (Human) 
2026-10-15 | PXD074969 | Pride
Phosphoproteomics Tio2 enrichment In vitro Transplant Antibody mediated rejection Galectin-1 Msstatsptm Easyphos protocol Primary human glomerular microvascular endothelial cells Sirna knockdown Interferon-gamma 
Proteomicsmsqrob2PTM: differential abundance and differential usage analysis of MS-based proteomics data at the post-translational modification and peptidoform level
In the era of open-modification search engines, more post-translational modifications than ever can be detected by LC-MS/MS-based proteomics. This development can switch proteomics research into a higher gear, as PTMs are key in many cellular pathways important in cell proliferation, migration, meta...
ORGANISM(S): Homo sapiens (Human) 
2024-06-16 | PXD043476 | Pride
Msqrob2ptm Ptm Msqrob Peptidoform 
ProteomicsA Nerve and Mast Cell Sentinel System Releases Extracellular Condensates to Induce Macrophage Repair
The peritoneal cavity has a higher density of immune cells then does blood. These cells are primarily localized within the bulk flow of fluid. As such, any perturbation within the peritoneum, ranging from a sterile injury to endometriosis to ovarian cancer, requires that the immune cells find a way ...
ORGANISM(S): Mus musculus (Mouse) 
2026-06-17 | PXD061150 | Pride
Granules Mouse Mast cell 
ProteomicsGuard Cell-Enriched Phosphoproteome from open and closed stomata
Control of the stomatal aperture is multifaceted, involving a complex interplay of environmental cues and intracellular signaling pathways. It is well established that changes in ion gradients drive water movement into and out of the guard cell, thereby altering cell volume and modulating the openin...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2026-05-22 | PXD070005 | Pride
Guard cell Plant Phosphorylation Endomembrane system Stomata Vacuole 
ProteomicsFAS Inhibited Proteomics and Phosphoproteomics Profiling of Colorectal Cancer Spheroids shows Activation of Ferroptotic Death Mechanism
Colorectal cancer (CRC) is projected to become the third most diagnosed and third most fatal cancer in the United States by 2024, with early onset CRC on the rise. Research is constantly underway to discover novel therapeutics for the treatment of various cancers to improve patient outcomes and surv...
ORGANISM(S): Homo sapiens (Human) 
2024-08-10 | PXD050987 | Pride
Phosphoproteomics Mass spectrometry Colorectal cancer Cancer Proteomics Data-independent acquisition Spheroids 
ProteomicsMultiplexed phosphoproteomics of low cell numbers using SPARCE
Understanding cellular diversity and disease mechanisms requires global analysis of proteins and their modifications. Ultrasensitive mass spectrometry-based proteomics enables unbiased protein-level analysis of low cell numbers, down to single cells. However, phosphoproteomics remains limited to hig...
ORGANISM(S): Homo sapiens (Human) 
2025-04-01 | PXD056902 | Pride
Tmt Glioblastoma Phospho Low-input 
ProteomicsGlobal proteomic and phosphoproteomic analysis of WT HEC-50B and MAPK14-/- HEC-50B cells cultured as 2D monolayers and 3D spheroids.
The molecular underpinnings of High Grade Endometrial Carcinoma (HGEC) metastatic growth and survival are poorly understood. Here we show that ascites-derived and primary tumor HGEC cell lines in 3D spheroid culture faithfully recapitulate key features of malignant peritoneal effusion and exhibit fu...
ORGANISM(S): Homo sapiens (Human) 
2025-10-07 | PXD053011 | Pride
Endometrial cancer P38a Mapk14 3d spheroids 
ProteomicsSecretome and phosphoproteome analysis of THP-1 and KOPN-8 cells treated with Insulin-like growth factor 2.
We describe the secretome and phosphoproteome of human leukemia cell lines, THP-1 and KOPN-8, treated with Insulin-like growth factor 2 (IGF2) using data-independent acquisition mass spectrometry analysis.
ORGANISM(S): Homo sapiens (Human) 
2024-04-02 | PXD049016 | Pride
Leukemia Secretome Extracellular Data-independent acquisition Phosphoproteome Igf2 
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