PXD069095

PXD069095 is an original dataset announced via ProteomeXchange.

Title	Limited proteolysis-coupled mass spectrometry captures proteome-wide protein structural alterations and biomolecular condensation in living cells
Description	To study protein structures directly within cells, we developed in-cell limited proteolysis-coupled mass spectrometry (in-cell LiP-MS). Conditions for introduction of proteinase K into human cells using electroporation were optimized and validated for intracellular cleavages. In-cell LiP-MS captured the known binding of rapamycin to FKBP1A within the cell and detected global protein structural alterations upon sodium arsenite treatment. It captured the structural dynamics of hundreds of proteins from biomolecular condensates with peptide level resolution and within live human cells such as structural alterations of individual sites on the involved proteins, such as known RNA-binding and intrinsically-disordered regions, and dissected the timing of the different events. We detected known and novel structural alterations of proteins from stress granules as well as from nuclear speckles and validated alteration of nuclear speckles by fluorescence microscopy. Our dataset provides a resource describing the structural changes of human proteins in response to cellular arsenite stress and pinpoints structurally altered regions. Further, comparison of LiP-based structural fingerprints before and after cell lysis revealed which human proteins are susceptible to structural change upon cell lysis, therefore guiding the design of future experiments requiring native protein structures.
HostingRepository	PRIDE
AnnounceDate	2025-11-10
AnnouncementXML	Submission_2025-11-10_15:51:17.141.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ludovic Gillet
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF; LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2025-10-02 13:33:32	ID requested
⏵ 1	2025-11-10 15:51:17	announced

Dataset with its publication pending

submitter keyword: stress granules, mass spectrometry, in-cell LiP, structural proteomics,Limited proteolysis, arsenite treatment, rapamycin

Paola Picotti
contact affiliation	Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
contact email	picotti@imsb.biol.ethz.ch
lab head
Ludovic Gillet
contact affiliation	ETH Zurich
contact email	gillet@imsb.biol.ethz.ch
dataset submitter

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://ftp.pride.ebi.ac.uk/pride/data/archive/2025/11/PXD069095

PRIDE project URI

• PRIDE
  1. PXD069095
     1. Label: PRIDE project
     2. Name: Limited proteolysis-coupled mass spectrometry captures proteome-wide protein structural alterations and biomolecular condensation in living cells