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ProteomicsAssessing the relationship between mass window width and retention time scheduling on protein coverage for data-independent acquisition
Due to the technical advances of mass spectrometers especially the high scanning speed and high MS/MS resolution, the data independent acquisition mass spectrometry (DIA-MS) began to be widely used, which enables high reproducibility in both proteomic identification and quantification. The current D...
ORGANISM(S): Homo sapiens (Human) 
2019-07-01 | PXD013477 | Pride
Scheduling Rtwindia Window size Oribtrap fusion lumos Dia-ms 
ProteomicsPhosphoproteomic analysis supporting structural basis for GABAA receptor pi activation
GABAA receptors (GABAAR) are pentameric chloride channels comprising various combinations of different subunits that are activated by γ-aminobutyric acid (GABA), the main inhibitory neurotransmitter in vertebrates. we show here that GABRP chloride channel activity and ERK signaling is directly regul...
ORGANISM(S): Homo sapiens (Human) 
2026-01-05 | PXD044482 | Pride
Phosphoproteomics Dia Gabaa receptor 
ProteomicsDeep Phosphoproteomic Elucidation of Metformin-Signaling in Heterogenous Colorectal Cancer Cells
The biguanide drug metformin is a safe and widely prescribed drug for type 2 diabetes. Interestingly, hundreds of clinical trials were set to evaluate the potential role of metformin in the prevention and treatment of cancer including colorectal cancer (CRC). However, the metformin-induced cell sign...
ORGANISM(S): Homo sapiens (Human) 
2023-02-18 | PXD036826 | Pride
Dia-ms Phosphoproteomics Metformin Colorectal cancer 
ProteomicsPhosphoproteomic analysis of signal transmission in the Mitotic Exit Network
In budding yeast, the Mitotic Exit Network (MEN), a GTPase signaling cascade integrates spatial and temporal signals to promote exit from mitosis. This signal integration requires transmission of a signal created on the cytoplasmic face of the spindle pole bodies (SPBs, functional equivalent of the ...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2021-01-14 | PXD020369 | Pride
Phosphoproteomics Dia-ms Yeast Mitotic exit 
ProteomicsBoxCarmax: a novel high-selectivity data-independent acquisition mass spectrometry method for the analysis of protein turnover and complex samples
The data-independent acquisition (DIA) mode performed in the latest high-resolution, high-speed mass spectrometers offers a powerful analytical tool for biological investigations. The DIA mass spectrometry (MS) combined with the isotopic labeling approach holds a particular promise for increasing th...
ORGANISM(S): Homo sapiens (Human) Rattus norvegicus (Rat) 
2021-02-02 | PXD021922 | Pride
Hela cells Dia Human plasma Serum starvation Pc12 cells 
ProteomicsProteomic and phosphoproteomic profilings in fibroblasts of 11 common mammalian species
A central goal of modern biology is to understand the molecular basis of phenotype evolution between species. Previously, the evolutionary profiling at the molecular level has been largely limited to the nucleotide level. Nevertheless, the genotype is translated to proteotype through comprehensive a...
ORGANISM(S): Bos taurus (Bovine) Sus scrofa (Pig) Homo sapiens (Human) Oryctolagus cuniculus (Rabbit) Canis lupus Monodelphis domestica Felis catus (Cat) (Felis silvestris catus) Rattus norvegicus (Rat) Ovis aries Macaca mulatta (Rhesus macaque) Equus caballus (Horse) 
2022-09-22 | PXD028979 | Pride
Phosphoproteomics Dia-ms Multiple species Quantitative proteomics 
ProteomicsQuantitative phosphoproteomics for nocodazole treated cells measured by Lumos DIA
Phosphoproteomic DIA-MS quantitative dataset for nocodazole treated cells (or “PhosDIA” in short). The MS samples injected in a previous publication for developing the IPF, an algorithm for identifying post-translationally modified peptides, were herein re-measured by a new, powerful Orbitrap Lumos ...
ORGANISM(S): Homo sapiens (Human) 
2020-06-08 | PXD017476 | Pride
Phosphoproteomics U2os cells Dia Nocodazle Lumos Cell cycle 
ProteomicsDIA-MS Detect the Dephosphorylation of Tau by Phosphorylation Targeting Chimera (PhosTAC)
Microtubule-associated protein tau is essential for microtubule assembly and stabilization. Hyperphosphorylation of the microtubule-associated protein tau plays an important pathological role in the development of Alzheimer’s disease and other tauopathies, one of the greatest unmet demands in the cl...
ORGANISM(S): Homo sapiens (Human) 
2023-03-16 | PXD037459 | Pride
Dephosphorylation Dia-ms Tau Phostac Phosphoproteomics 
ProteomicsHypothesis-free Illustration on How Phosphorylation Dynamically Impact Protein Turnover
The turnover measurement of proteins and proteoforms has been largely facilitated by the metabolic labeling coupled with mass spectrometry (MS), such as the dynamic Stable isotope labeling by amino acids in cell culture (SILAC) experiments, i.e., the dynamic SILAC or pSILAC approach. Very recent stu...
ORGANISM(S): Homo sapiens (Human) 
2022-12-01 | PXD037360 | Pride
Peptidoform Phosphorylation Protein turnover Clustering Deltasilac Dia-ms Pulse silac Data analysis Time course 
ProteomicsDIA-MS Detect the Targeted EGFR Dephosphorylation by Phosphorylation Targeting Chimera (PhosTAC)
Epidermal growth factor receptor (EGFR) is an important receptor tyrosine kinase protein. Activated EGFR promotes downstream signal transductions through phosphorylation, and its phosphorylation has been implicated in pathologies including many types of cancers. Previously, our lab has developed the...
ORGANISM(S): Homo sapiens (Human) 
2024-04-02 | PXD038022 | Pride
Phosphoproteomics Dia-ms Phostac Egfr Kinase 
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