Figure 1. Quantitative Proteomic and Phosphoproteomic Analysis of 110 Yeast Kinase and Phosphatase Deletion Strains.
(A) Experimental workflow. In total, 84 kinase and 26 phosphatase deletion strains were investigated, covering 82% of all viable yeast kinase and phosphatase deletion strains. Yeast were grown in duplicate under standard conditions and harvested at optical density 600 (OD600) ≈ 1.0. With SL-TMT-based (phospho) proteomics, >4,600 proteins and >13,000 phosphosites were quantified.
(B) Summary of the datasets. Bars show average numbers of molecules quantified per TMT11-plex and overlap of molecules quantified across 110 deletion strains. About 96% quantified phosphosites have protein quantifications and could be normalized by cognate protein ratios. Error bars indicate minimum and maximum numbers of molecules among 28 TMT11-plexes.
(C) Overview of the data analyses. Functional relationships between kinases and/or phosphatases were analyzed in three ways: (1) Gene Ontology enrichment analysis, (2) Δgene-Δgene correlation networks, and (3) molecule covariance networks.
(D) Hierarchical clustering analysis of a subset of 58 samples (see Figure S1F for full dendrogram). Biological duplicates clustered tightly. Deletion strains did not cluster with TMT groups or growth batches.
(E) GPD1 (a HOG1-dependent osmostress-induced protein) showed low levels in Δhog1, Δpbs2, and Δssk2. HOG1, SSK2, and PBS2 are MAPK components of the HOG pathway. PDA1 S313 showed decreased phosphorylation levels in strains lacking its known kinases (PKP1 and PKP2). Colored dots represent measurements in biological duplicate. Dashed lines indicate 3 SD cutoff (see the STAR Methods).