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ProteomicsProteomics needs better chromatography
Examination of relationship between chromatographic peak capacity and MS/MS scan rate.
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2016-12-13 | PXD004126 | Pride
Yeast Fusion lumos Shotgun 
ProteomicsRole of Ssd1 in modulating protein abundance in aneuploid wild yeast
We discovered that wild yeast strains can tolerate extra chromosomes, a condition known as aneuploidy, whereas well-studied laboratory strains cannot. Understanding why some cells can tolerate aneuploidy and others cannot could have far-reaching impact, as for example, 85% of solid tumors are aneup...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2020-01-17 | PXD013847 | Pride
Ssd1 Yeast Label-free proteomics Aneuploidy 
ProteomicsCARM1 substrate identification
The goal of the project was global identification of CARM1 substrates. Arginine methylation landscapes were profiled and compared in wild type and CARM1 knockout cells to determine in vivo substrates of CARM1.
ORGANISM(S): Homo sapiens (Human) 
2017-07-03 | PXD005871 | Pride
Mcf7 Mda-mb-231 Orbitrap fusion lumos Bottom-up Arginine methylation 
ProteomicsThe phosphoproteome response to dithiolthreitol in Saccharomyces cerevisiae
The project quantified the yeast phosphoproteome before and at various times after dithiolthreitol (DTT) in budding yeast, focusing on wild-type cells and mutants laking the Ire1 and Mkk1/Mkk2 kinases.
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2020-07-03 | PXD017396 | Pride
Stress Phosphoproteomic Salt stress Protein kinase a Dtt 
ProteomicsSalt stress phosphorylation network
We utilized high resolution, high mass accuracy quantitative proteomics to explore stress signaling in yeast. We accessed changes in protein phosphorylation at various time points after exposure to salt stress and used this information to reconstruct stress signaling networks. We performed similar e...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2018-04-05 | PXD006192 | Pride
Phosphorylation Yeast Environmental stress response Stress signaling 
ProteomicsMass spectrometry proteomics reveals proteins that function in mTOR regulated selective autophagy
We used proteomic profiling to identify proteins in the mTOR-autophagy axis. Mouse cell lines lacking individual autophagy genes (Atg5 or Ulk1/Ulk2) were treated with an mTOR inhibitor to induce autophagy and cultured in media with either glucose or galactose. Mass spectrometry proteome profiling re...
ORGANISM(S): Mus musculus (Mouse) 
2020-01-23 | PXD014990 | Pride
Selective autophagy  mtor  mass spectrometry proteomics  calcoco1  lc3  er-phagy  atg5  ulk1  ulk2 
ProteomicsProteomic studies of Escherichia coli CFT073 and MG1655
Here we dissected a regulatory network directed by the conserved iron homeostasis regulator, Ferric Uptake Regulator (Fur), in uropathogenic E. coli strain CFT073. Comparing anaerobic genome-scale Fur DNA binding, with Fur dependent transcript expression and protein levels of the uropathogen to that...
ORGANISM(S): Escherichia coli 
2020-05-27 | PXD017582 | Pride
Fur Upec Cft073 Iron regulation Ryhb Metabolic adaptation Ppgpp Sigma s 
ProteomicsRole of GATA-2 -77 enhancer in murine blood progenitor cells
We discovered enhancers that control GATA-2 expression during mouse development and in adult and generated mutant mouse strains that lack these enhancers, and these mice have very specific and important phenotypes that revealed GATA-2 mechanisms to control stem and progenitor cell transitions. In th...
ORGANISM(S): Mus musculus (Mouse) 
2020-06-05 | PXD013855 | Pride
Deep analysis Primary tissue Targeted proteomics Label-free proteomics 
ProteomicsMultiomic studies of inhibitory effects of lignocellulose-derived inhibitors on xylose utilization in Zymomonas mobilis using chemical defined synthetic hydrolysates
Previously we found that modified Zymomonas mobilis is able to convert glucose to ethanol when fermenting highly concentrated hydrolysates such as 9% glucan-loading AFEX-pretreated corn stover hydrolysate (ACSH), but that xylose conversion after glucose depletion is greatly impaired. We hypothesized...
ORGANISM(S): Zymomonas mobilis 
2019-10-28 | PXD015007 | Pride
Multiomics Microbial conversion Xylose metabolism Lignocellulosic hydrolysate Biofuels Zymomonas mobilis 
ProteomicsMouse Oncogenes Keratinocytes Proteomics
Raw files deposited for the mouse keratinocytes proteomics
ORGANISM(S): Mus Musculus (ncbitaxon:10090) 
2022-05-07 | MSV000089441 | MassIVE
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