To assign identities to the detected features, mzCloud and mzVault have been used to score fragmentation patterns and assign MS2-based identities. Additionally, an in-house developed MS_RT library was also used to support identification. Feature filtering parameters used were the following: Signal/noise > 3, mzCloud or mzVault match >50, ppm mass error within +/- 5ppm., match with in-house developed MS1_RT library within +/- 10sec., chromatographic peak and MS2 spectra quality were also considered.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - HILIC"],"chromatography_protocol":["The chromatographic separation was performed on a Thermo Vanquish Horizon UHPLC ((Thermo Scientific) equipped with a Waters Premier BEH Amide column (150mmx2.1mm, Waters), applying a gradient of 10mM ammonium bicarbonate in water (A) and 10mM ammonium bicarbonate in 95% acetonitrile (B) from 99% B to 30% B over 12min. The flow rate was 0.4ml/min, the column oven temperature 40°C, the autosampler temperature 5°C and the injection volume was 5ul.
"],"publication":["PKA regulates stress granule maturation to allow timely recovery after prolonged starvation."],"submitter_affiliation":["FGCZ","ETH Zürich"],"submitter_name":["Sonja Kroschwald","Martina Zanella"],"organism_part":["organism","mixture","solvent"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["After 2 hrs, the extraction solution was centrifuges at 15min, 4000rpm and 0 degree. The supernatant containing the metabolites was transferred to fresh tubes. Samples were dried in a Speed Vac and stored at minus 80 degree. Prior to MS analysis, samples were resuspended in 90 precent acetonitrile."],"organism":["blank","reference compound","Saccharomyces cerevisiae"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS13923"],"author":["Martina Zanella. Functional Genomics Center Zurich. Functional Genomics Center Zurich Winterthurerstr. 190, Y59 H38 8057 Zurich, Schweiz. martina.zanella@fgcz.ethz.ch. +41 44 635 39 25.","Alaa Othman. alaa.othman@fgcz.ethz.ch.","Matthias Peter. ETH Zurich. matthias.peter@ethz.ch.","Sonja Kroschwald. ETH Zurich. Otto-Stern-Weg 3, CH-8093 Zürich. sonja.kroschwald@bc.biol.ethz.ch. +41 446 336585."],"data_transformation_protocol":["The MS data generated with the untargeted approach were transformed and processed by means of the commercial software Compound Discoverer 3.3 (Thermo Fisher Scientific). The modular workflow includes spectra selection, retention times alignment, compound detection and grouping, gap filling, background filtering.
"],"study_factor":["Treatment","Timepoint"],"submitter_email":["martina.zanella@fgcz.ethz.ch","sonja.kroschwald@bc.biol.ethz.ch"],"sample_collection_protocol":["Cells were grown in synthetic media, inoculated at OD 0.2 and harvested after 6 days stationary phase, or additional 4,8, or 12hrs after re-feeding. Cells were harvested on a 0.45um pore size PVDF filter, which was then immediately frozen in a minus 20 degree cold extraction solution."],"omics_type":["Metabolomics"],"study_design":["ultra-performance liquid chromatography-mass spectrometry","comparative study","metabolomics study"],"curator_keywords":["ultra-performance liquid chromatography-mass spectrometry","comparative study","metabolomics study"],"mass_spectrometry_protocol":["The LC was coupled to Thermo Q Exactive mass spectrometer (Thermo Fisher Scientific) by a HESI source (spray voltage: 3500, capillary temperatute: 300°C, sheath gas: 30, aux gas: 10, spry current: 100, probe heater temperature: 250°C). MS1 (molecular ion) and MS2 (fragment) data were acquired using negative polarization and Full MS / dd-MS² (Top5) over a mass range of 70 to 1050 m/z (MS1 resolution of 70000, AGC target 1e6, max IT 100ms; MS2 resolution of 17’500, AGC target 1e5, max IT 50ms)
"],"additional_accession":[]},"is_claimable":false,"name":"PKA regulates stress granule maturation to allow timely recovery after prolonged starvation","description":"Cells have evolved multiple strategies to survive environmental stress conditions. This includes the formation of membrane-less cytoplasmic ribonucleoprotein structures called stress granules that sequester and protect mRNAs encoding many housekeeping genes. Stress granules are not static biomolecular condensates but transform into solid states during a maturation phase. The deposition of stress granule proteins in solid-like, insoluble aggregates is a hallmark of many neurodegenerative pathologies, thus studies to uncover the pathological link and mechanism underlying the stress granule maturation process are important. In this study we show that yeast stress granules mature into a solid-like state during long-term stationary phase stress, which delays stress granule disassembly and cell cycle restart. Profiling of phosphorylation sites during stationary phase revealed that stress granule maturation is driven by protein kinase A dependent phosphorylation of the stress granule proteome. Indeed, upon stationary phase the catalytic PKA subunits condense in stress granules, where stress granule-localized PKA kinase activity is maintained, whereas in parallel cytoplasmic-localized PKA activity is inhibited. PKA phosphorylates key stress granule components, including the pyruvate kinase Cdc19. Cdc19 phosphorylation by stress granule localized PKA is necessary and sufficient for its maturation in stress granules, where Cdc19 assembles into amyloid-like structures. Importantly, inhibiting PKA during long-term stationary phase prevents stress granule maturation, delaying ordered re-start of cell growth after re-feeding. Taken together, these results describe a stress granule maturation mechanism selectively activated during chronic stress that preserves stress granules integrity and promotes cell survival.","dates":{"publication":"2026-06-16","submission":"2026-02-19"},"accession":"MTBLS13923","cross_references":{}}