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ProteomicsS. cerevisiae DDA orbitrap-based benchmark datasets. C4PR_LIV
In this study, label free peptide intensities from a well quantitatively characterised yeast cell lysate were acquired on two orbitrap mass spectrometers (LTQ-Velos and Q Exactive HF). Additionally, samples containing Universal Proteomics Standard and the Proteomics Dynamic range Standard (http://ww...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2017-08-09 | PXD003472 | Pride
Peptide ionization Hydrophobicity Benchmark dataset Coelution Peptide detectability 
ProteomicsS. cerevisiae proteome response to heat stress - 240 min time course. C4PR_LIV
In this project, we follow the temporal proteome dynamics during heat stress response in a model organism Saccharomyces cerevisiae. Using label-free quantification we determine changes in the yeast proteome at different times after mild temperature shift, from 30˚C to 37˚C. The time points measured ...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2018-01-17 | PXD006262 | Pride
Environmental stress response Hsp70 chaperone Label free quantification 
ProteomicsA proteome-integrated, carbon source dependent genetic regulatory network in Saccharomyces cerevisiae
We propose a carbon source dependent genetic regulatory network for the budding yeast Saccharomyces cerevisiae, derived from quantitative proteomic analyses integrated with bioinformatics knowledge of regulatory pathways and protein interactions. The proposed network, comprising 1247 transcription f...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2021-03-22 | PXD009420 | Pride
Proteomics Shotgun proteomics Regulatory network Yeast S. cerevisiae 
ProteomicsProteogenomics Pipeline For Pineapple
Here we have undertaken a pilot study analysing the proteome of MD2 pineapple using Liquid Chromatography coupled with Mass Spectrometry (LC-MS/MS) and identified 3,818 peptides from 1,781 candidate proteins in the annotated V3 genome sequenced. In addition, a further 603 peptide identifications wer...
ORGANISM(S): Ananas comosus 
2024-05-24 | PXD045998 | Pride
Orbitrap elite Maxquant Pineapple Lc-ms/ms 
TranscriptomicsRIP-seq of Saccharomyces cerevisiae to identify RNAs which associate with members of the closed loop complex (eIF4E, eIF4GI, eIF4GII, Pab1p) and inhibtors of the complex (Caf20p, Eap1p)
The aim of this experiment was to look at RNAs which associate with members of the closed loop complex (eIF4E, eIF4GI, eIF4GII, Pab1p) and inhibtors of the complex (Caf20p, Eap1p) under optimal growth conditions in the Saccharomyces cerevisiae BY4741 strain background. NOTE: The csfasta and qual...
ORGANISM(S): Saccharomyces Cerevisiae 
2014-08-01 | E-MTAB-2464 | biostudies-arrayexpress
ProteomicsWhole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies
Our comprehensive model identifies condition-dependent and compartment-specific constraints that can explain metabolic strategies and protein expression profiles from growth rate optimization, providin a framework to understand metabolic adaptation in eukaryal cells.
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2022-01-24 | PXD030003 | Pride
Genetic regulation Ms/ms Metabolic networks 
TranscriptomicsEccentric exercise activates novel transcriptional regulation of hypertrophic signaling pathways
Full title: Eccentric exercise activates novel transcriptional regulation of hypertrophic signaling pathways not affected by hormone changes. Unaccustomed eccentric exercise damages muscle tissue stimulating mechanisms of recovery and remodeling that may be affected by cellular protection by the sex...
ORGANISM(S): Homo sapiens 
2009-12-16 | E-GEOD-19062 | biostudies-arrayexpress
TranscriptomicsRibo-seq analysis of Saccharomyces cerevisiae with and without 10 minute glucose starvation
Ribosome profiling (Ribo-Seq) and RNA-Seq analysis of Saccharomyces cerevisiae with and without 10 minute glucose starvation to determine effects on translation.
ORGANISM(S): Saccharomyces cerevisiae 
2021-09-30 | E-MTAB-9094 | biostudies-arrayexpress
ProteomicsIntegrated multi-omics reveals common properties underlying stress granule and P-body formation
Non-membrane-bound compartments such as mRNA processing bodies (PBs) and stress granules (SGs) play important roles in the regulation of gene expression following environmental stresses. We have systematically determined the protein and mRNA composition of PBs and SGs formed in response to a common ...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2021-11-03 | PXD018762 | Pride
Stress granule purification P-body purification Saccharomyces cerevisiae 
TranscriptomicsAnalysis of RIP-seq of Ded1 and eIF4A(Tif1) with and without glucose depletion
The aim of this experiment was to look at RNAs which associate with DEAD-box RNA helicases with and without 10 minutes of glucose starvation.
ORGANISM(S): Saccharomyces cerevisiae 
2021-09-30 | E-MTAB-9095 | biostudies-arrayexpress
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