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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 
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 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 
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 
ProteomicsData-independent Acquisition-based Proteome and Phosphoproteome Profiling across Six Melanoma Cell Lines
The rapid documentation of the steady-state gene expression landscape of the cells used in particular experiments may help to improve the reproducibility of scientific research. Here we applied a data-independent acquisition mass spectrometry (DIA-MS) method, coupled with a peptide spectral-library ...
ORGANISM(S): Homo sapiens (Human) 
2021-03-15 | PXD022992 | Pride
Melanoma Proteome Cell lines Dia Metastasis Phosphoproteome 
ProteomicsGlobal and site-specific effect of phosphorylation on protein turnover
The effects of specific modification types and sites on protein lifetime have not been illustrated in large scale. We describe a proteomic method, DeltaSILAC, to quantify the impact of site-specific phosphorylation on the turnover of thousands of proteins in live cells. Being configured on the accur...
ORGANISM(S): Homo sapiens (Human) Rattus norvegicus (Rat) 
2020-11-17 | PXD017496 | Pride
Phosphoproteomics Cell line Dia Turnover Lumos 
ProteomicsAn Integrative Transcriptome – Proteome Approach Reveals a Robust Expression Pattern of Small Intestinal Epithelial Organoids from Germ-Free and Microbiota Associated Donors
Intestinal epithelial organoids established from resected gut tissue have become a widely used research tool. However, it remains unclear how environmental cues and other sources of variation before, during and after establishment impact on organoid properties. Divergent microbiota composition in se...
ORGANISM(S): Mus musculus (Mouse) 
2020-03-05 | PXD016339 | Pride
Intestinal epithelial organoids  swath  5600 
ProteomicsImpact of alternative splicing on the human proteome
Alternative splicing is a critical determinant of genome complexity and by implication, is assumed to engender proteomic diversity. This notion has not been experimentally tested in a targeted, quantitative manner. Here, we have developed an integrative approach to ask whether dynamic perturbations ...
ORGANISM(S): Homo sapiens (Human) 
2017-08-02 | PXD003278 | Pride
Alternative splicing Swath Proteome Prpf8 
ProteomicsMulti-omic measurements of heterogeneity in HeLa cells across laboratories
We collected 14 stock Hela aliquots from 13 different laboratories across the globe and cultured them in the same conditions. We extensively profiled the genome-wide copy numbers, mRNAs, proteins, protein turnover rates by genomics techniques and the highly reproducible and accurate proteomic method...
ORGANISM(S): Homo sapiens (Human) 
2019-02-11 | PXD009273 | Pride
Reproducibility Hela cells Swath-ms 
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