Fig. 1

a Cartoon illustrating the HOG pathway. Its central module consists of the MAPK Hog1, the MAPK kinase (MAPKK) Pbs2, and the three MAPKK kinases (MAPKKK) Ste11, Ssk2, and Ssk22. Upon activation by extracellular hyperosmolarity, Hog1 coordinates the osmostress response by phosphorylating its target proteins. Ultimately, the cascade leads to the activation of downstream kinases, such as Rck2. b Illustration of experimental conditions from Romanov et al., 2017 [4]. c Illustration of study concept. d Box- and density plot showing the degree of overlap in % of identified peptides (grey) and phosphorylated peptides (red) between PD and MQ outputs for each raw file (dot). Black line in box plot indicates median overlap (e) Venn diagrams showing percentage and total number of quantified peptides, quantified phosphorylation sites and proteins identified by MQ (light blue), PD (yellow) or both (green). f Correlation of SILAC log₂-ratios of mutually quantified phosphorylation sites of setup SR. Lines indicate limits of +/− 1 quantification difference (g) Histogram displaying quantification difference calculated as MQ/PD SILAC-ratio [log₂] of quantified phosphorylation sites of setup SR. Lines indicate cut-off (+/− 1 quantification difference)