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Total Proteome Analysis in RNAi treated C. elegans (mrps5, fzo1, drp1, eat3)

ABSTRACT: A SWATH-based worflow has been developed for C. elegans proteome profiling, including sample preparation, SWATH spectral library generation and downstream data treatment. The influences of several RNAi treatments (including mrps5, fzo1, drp1, eat3) on C. elegans total proteome were studied.

INSTRUMENT(S): TripleTOF 6600

ORGANISM(S): Caenorhabditis Elegans

TISSUE(S): Whole Body

SUBMITTER: Evan Williams

LAB HEAD: Ruedi Aebersold

PROVIDER: PXD009256 | Pride | 2020-04-03

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	Celegans_cirt_in_house_combined_clean.TraML	Other
	E1803191030_feature_alignment_requant.tsv.gz	Tabular
	E1803191030_matrix.xlsx	Xlsx
	wevan_I171125_Jiayi_HT115_L4_Run02.wiff	Wiff
	wevan_I171125_Jiayi_HT115_L4_Run02.wiff.scan	Wiff

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Publications

Mitochondrial translation and dynamics synergistically extend lifespan in C. elegans through HLH-30.

Liu Yasmine J YJ McIntyre Rebecca L RL Janssens Georges E GE Williams Evan G EG Lan Jiayi J van Weeghel Michel M Schomakers Bauke B van der Veen Henk H van der Wel Nicole N NN Yao Pallas P Mair William B WB Aebersold Ruedi R MacInnes Alyson W AW Houtkooper Riekelt H RH

The Journal of cell biology 20200601 6

Mitochondrial form and function are closely interlinked in homeostasis and aging. Inhibiting mitochondrial translation is known to increase lifespan in C. elegans, and is accompanied by a fragmented mitochondrial network. However, whether this link between mitochondrial translation and morphology is causal in longevity remains uncharacterized. Here, we show in C. elegans that disrupting mitochondrial network homeostasis by blocking fission or fusion synergizes with reduced mitochondrial translat ...[more]

PMID: 32259199

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Total Proteome Analysis in RNAi treated C. elegans

Project description:A SWATH-based worflow has been developed for C. elegans proteome profiling, including sample preparation, SWATH spectral library generation and downstream data treatment. The influence of mrps-5 RNAi treatment on C. elegans total proteome were studied.

2019-12-11 | PXD009223 | Pride

7q11.23 CNV altered proteome in iPSC differentiating neurons

Project description:Copy number variations (CNVs) at 7q11.23 cause Williams-Beuren (WBS) and 7q microduplication syndromes (7Dup), two neurodevelopmental disorders with shared and opposite cognitive-behavioral phenotypes. Using patient-derived and isogenic neurons, we integrated transcriptomics, translatomics and proteomics to elucidate the molecular underpinnings of this dosage effect. We found that 7q11.23 CNVs cause opposite alterations in neuronal differentiation and neuronal excitability. Here, the 7q11.23 CNV altered proteome in iPSC differentiating neurons was measured by a fast SWATH-MS method.

2024-10-17 | PXD038156 | Pride

Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS: PTM-SWATH-MS Gold Standard data set

Project description:The PTM-SWATH MS Gold Standard data set consists of a previously published (Soste et al., 2014, PMID:25194849) set of 579 unpurified, synthetic, heavy-isotope labeled phosphopeptides (Thermo Scientific Biopolymers). These phosphopeptides represent biologically relevant sequences from S. cerevisiae proteins, which have been found altered in their phosphorylation status under various conditions. The complete peptide set contains a mixture of singly and doubly phosphorylated sequences with in average more than 3 modifiable residues per peptide (serines, threonines or tyrosins, often in close proximity to each other). All peptides were mixed with equal volumes (concentrations are unknown due to the unpurified status of the peptides) and the resulting peptide mix was either analyzed directly in DDA mode for assay library generation or spiked into a human cell line background proteome in a 13-step dilution series and analyzed in SWATH mode for the generation of the SWATH Gold Standard data set.

2017-06-12 | PXD004573 | Pride

Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS: Phosphopeptide-enriched data set

Project description:This data set represent an experiment comparing enriched phosphopeptides of a human U2OS cell line. Phosphopeptide-enriched samples of ten nocodazole treated and ten control U2OS cell line samples were acquired each in DDA and DIA (SWATH-MS) modes.

2017-06-12 | PXD006056 | Pride

Impact of alternative splicing on the human proteome

Project description: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 in mRNA splicing patterns that follow depletion of the core spliceosome factor PRPF8 alter the composition of the proteome. We integrate RNA-sequencing (to comprehensively report intron retention, differential transcript usage and gene expression) with a newly developed data-independent acquisition (DIA) method, SWATH-MS (Sequential Window Acquisition of all THeoretical spectra – mass spectrometry), to capture an unbiased and quantitative snapshot of constitutive and alternative splicing events at the protein level. Whereas intron retention is accompanied by decreased protein abundance, dynamic alterations in differential transcript usage and gene expression alter protein abundance proportionally to transcript levels. Our findings exemplify how RNA splicing exerts a pervasive effect linking isoform expression in the human transcriptome with proteomic diversity, and provide a toolkit for studying its perturbation in human diseases.

2017-08-02 | PXD003278 | Pride

Yeast Nat Nt-acetylation SWATH MS

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2020-12-15 | PXD015217 | Pride

From coarse to fine: The absolute Escherichia coli proteome under diverse growth conditions

Project description:Accurate measurements of cellular protein concentrations are invaluable to quantitative studies of gene expression and physiology in living cells. Here, we developed a versatile mass spectrometric workflow based on data-independent acquisition proteomics (DIA/SWATH) together with a novel protein inference algorithm (xTop). We used this workflow to accurately quantify absolute protein abundances in E. coli for >2000 proteins over >60 growth conditions, including nutrient limitations, non-metabolic stresses and non-planktonic states. The resulting high-quality dataset of protein mass fractions allowed us to characterize proteome responses from a coarse (groups of related proteins) to a fine (individual) protein level. Hereby, a plethora of novel biological findings could be elucidated, including the generic upregulation of low-abundant proteins under various metabolic limitations, the non-specificity of catabolic enzymes upregulated under carbon limitation, the lack of larg e-scale proteome reallocation under stress compared to nutrient limitations, as well as surprising strain-dependent effects important for biofilm formation. These results present valuable resources for the systems biology community and can be used for future multi-omics studies of gene regulation and metabolic control in E. coli.

2021-03-11 | PXD014948 | Pride

Quantitative variability of 342 plasma proteins in a human twin population

Project description:The human plasma proteome is clinically highly significant and has been studied extensively because it is thought that its molecular makeup provides a window into the health state of an individual. However, neither the quantitative variability of the plasma proteome nor the origins of the variation are known. To determine the relative contributions of heritability, environmental and longitudinal factors to plasma proteome variability we systematically decomposed the biological variance of 1904 peptides defining 342 unique plasma protein profiles from 232 plasma samples that were collected with 2-7 year intervals from monozygotic (MZ) and dizygotic (DZ) twins. The data were collected via SWATH mass spectrometry (SWATH-MS), an emerging technology characterized by high degree of reproducibility and quantitative accuracy. The data indicate abundance variability is an important feature for different proteins among population, that the abundances of about 20% of plasma protein are considerably heritable, and that the degrees of genetic control and aging effects vary across specific biological processes. Moreover, we identified 13 cis- SNPs significantly influencing the abundance level of specific plasma proteins. These results substantially extend the understanding of the impact of heritability on the human proteomic dynamics and therefore have implications for the effective design of plasma-based biomarker studies.

2015-01-05 | PXD001064 | 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

Proteome dysregulation in Down syndrome reveals organelle specific aberrations

Project description:Human Trisomy 21 (T21), which causes Down Syndrome (DS), is the most common known cause of intellectual disability. However, the molecular basis for DS phenotypic variability remains poorly understood. Here we used SWATH mass spectrometry (SWATH-MS) to quantify protein abundance and protein turnover in fibroblasts from a monozygotic twin pair discordant for T21, and to profile protein expression in 11 unrelated DS individuals and age-matched controls. The integration of the steady state and turnover proteomic data sets with transcript profiles indicated that protein-specific degradation of members of stoichiometric complexes presents a major determinant of T21 gene dosage outcome, a primary effect that was not apparent from genomic data. The data also reveal that T21 results in extensive proteome remodeling similarly affecting proteins encoded by all chromosomes. Finally, we found broad, organelle-specific posttranscriptional effects such as significant down-regulation of the mitochondrial proteome contributing DS hallmarks and variability.

2017-11-01 | PXD004880 | Pride