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ProteomicsSimPLIT: Simplified sample preparation for large-scale isobaric tagging proteomics
Large scale proteomic profiling of cell lines can yield valuable insights into the molecular signatures attributed to variable genotypes or induced perturbations. Specifically, the ability to perform deep and rapid proteome analysis of pharmacologically modulated cells could generate drug-protein as...
ORGANISM(S): Homo sapiens (Human) 
2022-08-03 | PXD031510 | Pride
Tmtpro Imids Celmods Targeted protein degradation Cancer cell lines Isobaric labeling 
ProteomicsSimPLIT: Simplified sample preparation for large-scale isobaric tagging proteomics
Large scale proteomic profiling of cell lines can yield valuable insights into the molecular signatures attributed to variable genotypes or induced perturbations. Specifically, the ability to perform deep and rapid proteome analysis of pharmacologically modulated cells could generate drug-protein as...
ORGANISM(S): Homo sapiens (Human) 
2022-08-03 | PXD034022 | Pride
Imids Tmtpro Celmods Targeted protein degradation Cancer cell lines Isobaric labeling 
ProteomicsQuantitative proteomics of U2O2 cells in asynchronous or synchronized in late mitosis
U2OS cells were either asynchronous or synchronized in late mitosis (anaphase/telophase) prior to irradiation. Asynchronous cells were grown to 75–80% confluence, irradiated with 4 Gy, and collected 5–10 minutes later. For synchronized samples, cells were subjected to a thymidine block, released int...
ORGANISM(S): Homo sapiens (Human) 
2026-03-18 | PXD064722 | Pride
U2o2 cell Irradiation Mitosis Quantitative proteomics 
MetabolomicsDeep longitudinal multi-omics analysis of Bordetella pertussis cultivated in bioreactors highlights medium starvations and transitory metabolisms, associated to vaccine antigen biosynthesis variations and global virulence regulation

Bordetella pertussis is the bacterial causative agent of whooping cough, a serious respiratory illness. An extensive knowledge on its virulence regulation and metabolism is a key factor to ensure pertussis vaccine manufacturing process robustness. The aim of this study was to refine our ...

2023-02-21 | MTBLS5762 | MetaboLights
ProteomicsQuantitative proteomic analysis of Shigella flexneri and Shigella sonnei Generalized Modules for Membrane Antigens (GMMA) reveals highly pure preparations.
Shigella flexneri 2a and Shigella sonnei were genetically modified to shed large quantities of outer membrane blebs. The blebs, called Generalized Modules for Membrane Antigens (GMMA), were purified and the protein content was estimated using the label-free iBAQ procedure. There were 2308 proteins i...
ORGANISM(S): Shigella flexneri 2a str. 2457T Shigella sonnei 53G 
2016-01-12 | PXD002517 | Pride
Shigella flexneri Label-free quantification Shigella sonnei. lc-ms/ms 
ProteomicsE2~dID: A versatile approach to identify substrates modified with ubiquitin and ubiquitin-like molecules by specific E3 enzymes
Covalent modifications of proteins with ubiquitin and ubiquitin-like molecules are instrumental to most, if not all biological processes. However, identifying the E3 ligase responsible for these modifications remains a major bottleneck in ubiquitin research. Here, we have developed an E2-thioester-d...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2019-04-03 | PXD008624 | Pride
Ubiquitin Ap-ms Tmt 
ProteomicsFeatureFinderIdentification (OpenMS) analysis of the iPRG-2015 dataset
Benchmark of FeatureFinderIdentification (FFId), a targeted feature detection algorithm for use in label-free quantification, developed in the OpenMS software framework. The dataset used for the evaluation comes from the iPRG-2015 study ("Differential abundance analysis in label-free quantitative pr...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2017-07-07 | PXD006336 | Pride
Iprg-2015 Label-free quantification Feature detection Benchmark Shotgun proteomics 
ProteomicsMolecular signatures after challenge with Salmonella Typhi implicate host tryptophan metabolism in the pathogenesis of typhoid fever, part 1
Induced pluripotent stem (iPS) cell derived human macrophages were stimulated with IFN-y or exposed to viable S. Typhimurium SL1344 using either a gentamicin invasion assay or after over-night priming with IFN-y. Protein abundance changes between samples was determined relative to unstimulated contr...
ORGANISM(S): Homo sapiens (Human) 
2016-05-31 | PXD001953 | Pride
Human Macrophages Salmonella typhi Tmt Ips 
ProteomicsCancer-associated FBXW7 loss is synthetic lethal with pharmacological targeting of CDC
The FBXW7 tumour suppressor is commonly mutated, deleted or hypermethylated in a variety of cancer histologies. The tumour suppressive role of the FBXW7 protein has been ascribed to its ability to drive the ubiquitination and degradation of oncoproteins via its role as a substrate recognition subuni...
ORGANISM(S): Homo sapiens (Human) 
2024-06-16 | PXD043904 | Pride
Cdc Fbxw7 Synthetic lethal 
ProteomicsComprehensive proteomic profiling of the differences between Cancer Associated Fibroblasts and KRAS mutated cancer cell lines
Cancer associated fibroblasts (CAFs) are a key component of tumors. We aimed to profile the proteome of cancer cell lines representing three common cancer types (lung, colorectal and pancreatic) and a representative CAF cell line from each tumor type to gain insight into CAF function and identify ne...
ORGANISM(S): Homo sapiens (Human) 
2024-08-22 | PXD054500 | Pride
Cancer associated fibroblasts Kras Cafs 
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