MassIVE MSV000090634

Partial Public PXD037887

Stress granules proteome composition

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Description

Analysis of stress granules in HeLa cells, after exposure to different stimuli. Granules were collected by a newly devised enrichment method, described in manuscript. Proteomics sample preparation of granules was carried out using the Single-pot, solid phase-enhanced sample preparation, SP3 method (Hughes CS et al. Nat Protoc 14, 68 85 (2019)). Desalting, clean-up and loading to the MS was done using an Evosep one EV1000 instrument, following manufacturers protocol, but loading of sample to Evotips was done a pre-existing volume of A Buffer. Samples were measured on a Thermo Exploris 480 mass spectrometer, using data-independent acquisition (DIA) (30 SPD, 44 LC min gradient (Evosep), MS1: 120000 res, 350-1400 m/z, inj. time 50 ms, MS2: 14 m/z isolation windows, 1 /mz overlap, precursor mass range. 350-1020 m/z, stepped collision energy 25,27.5,30, 22 ms inj. time. RAW files were analyzed using Spectronaut v16, using directDIA mode with default settings, using as database the Homo Sapiens EBI Reference proteome, downloaded on 03/2021 and including an in-house curated contaminants list based on the MaxQuant's contaminants list. Protein summarisation was done with MSstats, using default settings. [doi:10.25345/C53B5WC9T] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: stress granules

Contact

Principal Investigators:
(in alphabetical order) 		Gerhard Mittler, Max Planck Institute of Immunobiology and Epigenetics, Germany
Submitting User: agomeza

Publications

Zhou Y, Panhale A, Shvedunova M, Balan M, Gomez-Auli A, Holz H, Seyfferth J, Helmstädter M, Kayser S, Zhao Y, Erdogdu NU, Grzadzielewska I, Mittler G, Manke T, Akhtar A.
RNA damage compartmentalization by DHX9 stress granules.
Cell. 2024 Mar 28;187(7):1701-1718.e28. Epub 2024 Mar 18.

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