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The regulatory landscape of the yeast phosphoproteome – quantitative phosphoproteomic DIA data

ABSTRACT: We systematically exposed the yeast Saccharomyces cerevisiae to a wide array of 101 perturbations and generated a quantitative mass spectrometry-based atlas of early phosphoproteomic responses. Perturbations covered broad classes of environmental, chemical, and drug perturbations and systematically targeted diverse aspects of yeast cell biology. Importantly, most perturbations focused on capturing early signaling responses (5 min treatments), with the reasoning that functional phosphorylation of specific substrates occurs rapidly following stimulation, but promiscuous phosphorylation and confounding changes in transcript and protein abundances takes place more slowly. Treatments were done in 6 biological replicates and large-scale phosphoproteomics was enabled by our recently developed R2-P2 (Rapid-Robotic Phosphoproteomics) sample preparation workflow in combination with DIA measurements. This submission includes 559 quantitative phospho DIA-MS raw files that went into the analysis of the systems-level phosphorylation stress response.

INSTRUMENT(S): Orbitrap Exploris 480

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

SUBMITTER: Mario Leutert

LAB HEAD: Judit Villén

PROVIDER: PXD035050 | Pride | 2023-08-27

REPOSITORIES: Pride

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			Action	DRS
	cerevisiae_orf_trans_all.fasta	Fasta
	identifications_overview.tsv	Tabular
	precursor_quantifications.tsv	Tabular
	sample_annotations.xlsx	Xlsx
	spectral_library.kit	Other

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The regulatory landscape of the yeast phosphoproteome – quantitative proteomics DIA data

Project description:We systematically exposed the yeast Saccharomyces cerevisiae to a wide array of 101 perturbations and generated a quantitative mass spectrometry-based atlas of early phosphoproteomic responses. Perturbations covered broad classes of environmental, chemical, and drug perturbations and systematically targeted diverse aspects of yeast cell biology. Importantly, most perturbations focused on capturing early signaling responses (5 min treatments), with the reasoning that functional phosphorylation of specific substrates occurs rapidly following stimulation, but promiscuous phosphorylation and confounding changes in transcript and protein abundances takes place more slowly. Large-scale proteomics and phosphoproteomics was enabled by our recently developed R2-P2 (Rapid-Robotic Phosphoproteomics) sample preparation workflow in combination with DIA measurements. In parallel to phosphoproteomic measurements we performed total proteome measurements on the same samples for 30 selected perturbations. This submission includes 126 quantitative DIA-MS raw files that were used for the total proteome analysis.

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