Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Yeast proteomic analysis upon temperature shift

ABSTRACT: DIA/SWATH analysis of yeast upon temperature shift.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Ludovic Gillet

LAB HEAD: Ruedi A Aebersold

PROVIDER: PXD016320 | Pride | 2021-06-28

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ConsLib_6600_Yeast_TempStability.sptxt	Other
	ConsLib_6600_Yeast_TempStability_openswath_curated.csv	Csv
	E1610132312_feature_alignment.tsv	Tabular
	FileAnnotation.xlsx	Xlsx
	iProphet_Comet_Mascot_Yeast_TempStability.pep.xls	Xls

Items per page:

1 - 5 of 30

Publications

Puf6 primes 60S pre-ribosome nuclear export at low temperature.

Gerhardy Stefan S Oborská-Oplová Michaela M Gillet Ludovic L Börner Richard R van Nues Rob R Leitner Alexander A Michel Erich E Petkowski Janusz J JJ Granneman Sander S Sigel Roland K O RKO Aebersold Ruedi R Panse Vikram Govind VG Panse Vikram Govind VG

Nature communications 20210804 1

Productive ribosomal RNA (rRNA) compaction during ribosome assembly necessitates establishing correct tertiary contacts between distant secondary structure elements. Here, we quantify the response of the yeast proteome to low temperature (LT), a condition where aberrant mis-paired RNA folding intermediates accumulate. We show that, at LT, yeast cells globally boost production of their ribosome assembly machinery. We find that the LT-induced assembly factor, Puf6, binds to the nascent catalytic R ...[more]

PMID: 34349113

Similar Datasets

Yeast Nat Nt-acetylation SWATH MS

Project description:Yeast strains (wild type, Naa10 KO and Naa20 KO, resp: wt, natA-delta and natB-delta) were profiled for full proteome analysis by SWATH MS

2020-12-15 | PXD015217 | Pride

A primary human T-cell spectral library to facilitate large scale quantitative T-cell proteomics

Project description:Comprehensive spectral libraries are essential in sequential window acquisition of all theoretical mass spectra (SWATH-MS) based high throughput proteomic studies. Even though SWATH-MS assays provide robust quantitative proteomics data its applications to human T-cell studies are limited by the lack of a human T-cell spectral library. To address this resource gap, we generated a high-quality spectral library containing data for 3,941 unique proteins from primary human T-cells across genetically unrelated donors. SWATH-MS analysis of 18 primary T-cell samples using the new human T-cell spectral library identified and quantified 3,022 proteins at 1% FDR, whereas the larger Pan-human spectral library identified and quantified 2,794 proteins, with only 34% overlap. Combining the two libraries resulted in 4,061 proteins, covering ~50% of proteins in immune-related pathways. Overall, this data suggests DDA-MS is suited to discovery projects through to its enhanced sensitivity and SWATH-MS is suited to high-throughput projects.

2020-10-19 | PXD019446 | Pride

Dynamic of the Grb2 interactome in primary cells by DDA-MS

Project description:We applied AP-MS to quantify Grb2 interaction dynamics in primary T cells. Data generated here in shotgun/DDA mode were used to build a high quality Grb2 binders-specific SWATH assay library for high-throughput targeted analysis of DIA data.

2017-03-09 | PXD003973 | Pride

DDA files of human cancer cells for the NCI-60 SWATH project PXD003539

Project description:This is the raw files for the DDA library used for intepreting the NCI-60 SWATH project PXD003539

2019-10-21 | PXD009597 | Pride

The GTPase Nog1 co-ordinates assembly, maturation and quality control of distant ribosomal functional centers

Project description:Yeast ribosome assembly analysis, using APMS on various 60S tagged subunits (SSF1, RIX1, ARX1, KRE35, ARX1_bud20D, KRE35_DRG1, KRE35_drg-dn, YEP, G223, NOG1)

2020-01-06 | PXD011382 | Pride

Enterococcus faecalis V583, Part 1

Project description:Genome-scale models represent the link between an organism's genetic information and experimentally observable biological phenotypes. They facilitate metabolic engineering and the discovery of network properties such as the identification of novel drug targets. Most commonly, metabolite consumption data is used to limit the solution space, sometimes in combination with gene expression data. However, information about gene expression only poorly correlates with the abundance of the respective proteins within the cell. As such, we developed a method to map and integrate the whole-cell proteome into genome-scale models on the example of lactic acid bacteria (LAB). To the best of our knowledge, this work represents the first effort to integrate proteome data into genome-scale models on such a scale.

2016-12-06 | PXD001576 | Pride

Comparative analysis of mRNA degradation and protein degradation in 68 pairs of adjacent prostate tissue samples indicates high stability of proteins

Project description:Here we investigated the degradation of mRNA and protein in 68 pairs of adjacent prostate tissue samples using RNA-seq and pressure cycling technology (PCT) coupled with SWATH mass spectrometry and developed a score, the Proteome Integrity Number (PIN), to quantify the extent of protein degradation in the samples.

2019-06-12 | PXD007841 | Pride

∆glnA Enterococcus faecalis V583 - data analysis

Project description:A group of gram positive bacteria that share the characteristic of fermenting hexose sugars to lactic acid are generally referred to as lactic acid bacteria (LAB). Enterococcus faecalis is one of the widely studied LABs due to a multiutude of reasons. On the one hand, it plays an important role in dairy industry, being for example a starter in cheese cultures. On the other hand, it accounts for a large part of the infections caused by the LABs in hospital environments. During the past few years, it developed resistance against most of the major antibiotics. Here, in an attempt to study its adaptive metabolism, a glutamine synthetase mutant (∆glnA) of E. faecalis was subjected to pH shift and the results from the integrative analysis of its metabolic network were compared to those of the wild type. The proteome data generated in this study were used to constrain the genome-scale metabolic network at two pH level, aiming to reduce the solution space and improve the accuracy of model simulation. This data particularly helped to come up with a new design for the amino acid transport system in the genome-scale model, resulting in an accurate reproduction of the metabolic behaviour of E. faecalis.

2022-01-14 | PXD030778 | Pride

Enterococcus faecalis V583 - data analysis

2016-12-06 | PXD002869 | Pride

Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS: Twin blood plasma quantitative variance components

Project description:This data set represents a reanalysis of human blood plasma samples measured by SWATH-MS of 36 pairs of monozygotic and 22 pairs of dizygotic twins that were sampled at two longitudinal time points (Liu et al., 2015, PMID:25652787). The data were used to determine the overall quantitative variability of 4322 peptidoforms in the sample cohort and to assign the measured variability to heritability, environmental or longitudinal effects.

2017-06-06 | PXD004574 | Pride