PXD037887

PXD037887 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Stress granules proteome composition
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.
HostingRepository	MassIVE
AnnounceDate	2025-08-12
AnnouncementXML	Submission_2025-08-12_08:35:15.627.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alejandro Gomez-Auli
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	Oxidation
Instrument	Orbitrap Exploris 480

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2022-11-02 17:47:57	ID requested
⏵ 1	2025-08-12 08:35:16	announced

Publication List

Zhou Y, Panhale A, Shvedunova M, Balan M, Gomez-Auli A, Holz H, Seyfferth J, Helmst, ä, dter M, Kayser S, Zhao Y, Erdogdu NU, Grzadzielewska I, Mittler G, Manke T, Akhtar A, RNA damage compartmentalization by DHX9 stress granules. Cell, 187(7):1701-1718.e28(2024) [pubmed]

Zhou Y, Panhale A, Shvedunova M, Balan M, Gomez-Auli A, Holz H, Seyfferth J, Helmst, ä, dter M, Kayser S, Zhao Y, Erdogdu NU, Grzadzielewska I, Mittler G, Manke T, Akhtar A, RNA damage compartmentalization by DHX9 stress granules. Cell, 187(7):1701-1718.e28(2024) [pubmed]

Keyword List

submitter keyword: stress granules

submitter keyword: stress granules

Contact List

Gerhard Mittler
contact affiliation	Max Planck Institute of Immunobiology and Epigenetics
contact email	mittler@ie-freiburg.mpg.de
lab head
Alejandro Gomez-Auli
contact affiliation	Max Planck Institute of Immunobiology and Epigenetics
contact email	gomez@ie-freiburg.mpg.de
dataset submitter

Full Dataset Link List

MassIVE dataset URI
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MassIVE dataset URI

Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://massive-ftp.ucsd.edu/v05/MSV000090634/