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Cell Commun Signal. 2019 Jun 17;17(1):66. doi: 10.1186/s12964-019-0381-z.

Novel interconnections of HOG signaling revealed by combined use of two proteomic software packages.

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Department of Biochemistry, Max F. Perutz Laboratories, Vienna BioCenter, Vienna, Austria.
Children's Cancer Research Institute, St. Anna Kinderspital, Vienna, Austria.
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
Current Address: Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438, Frankfurt am Main, Germany.
Mass Spectrometry Facility, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter, Vienna, Austria.
Mass Spectrometry Facility, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter, Vienna, Austria.


Modern quantitative mass spectrometry (MS)-based proteomics enables researchers to unravel signaling networks by monitoring proteome-wide cellular responses to different stimuli. MS-based analysis of signaling systems usually requires an integration of multiple quantitative MS experiments, which remains challenging, given that the overlap between these datasets is not necessarily comprehensive. In a previous study we analyzed the impact of the yeast mitogen-activated protein kinase (MAPK) Hog1 on the hyperosmotic stress-affected phosphorylome. Using a combination of a series of hyperosmotic stress and kinase inhibition experiments, we identified a broad range of direct and indirect substrates of the MAPK. Here we re-evaluate this extensive MS dataset and demonstrate that a combined analysis based on two software packages, MaxQuant and Proteome Discoverer, increases the coverage of Hog1-target proteins by 30%. Using protein-protein proximity assays we show that the majority of new targets gained by this analysis are indeed Hog1-interactors. Additionally, kinetic profiles indicate differential trends of Hog1-dependent versus Hog1-independent phosphorylation sites. Our findings highlight a previously unrecognized interconnection between Hog1 signaling and the RAM signaling network, as well as sphingolipid homeostasis.


High-osmolarity glycerol (HOG); Hog1; Hyperosmotic stress response; Kic1; MaxQuant; Mitogen-activated protein kinase (MAPK); ORMDL; Orm2; Proteome discoverer; Proteomics; p38

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