PXD055783

PXD055783 is an original dataset announced via ProteomeXchange.

Title	Analysis of limited proteolysis-coupled mass spectrometry data
Description	Limited proteolysis combined with mass spectrometry (LiP-MS) facilitates probing structural changes on a proteome-wide scale. This method leverages differences in the proteinase K accessibility of native protein structures to concurrently assess structural alterations for thousands of proteins in situ. Distinguishing different contributions to the LiP-MS signal, such as changes in protein abundance or chemical modifications, from structural protein alterations remains challenging. Here, we present the first comprehensive computational pipeline to infer structural alterations for LiP-MS data using a two-step approach. (1) We remove unwanted variations from the LiP signal that are not caused by protein structural effects and (2) infer the effects of variables of interest on the remaining signal. Using LiP-MS data from three species we demonstrate that this approach outperforms previously employed approaches. Our framework provides a uniquely powerful approach for deconvolving LiP-MS signals and separating protein structural changes from changes in protein abundance, post-translational modifications and alternative splicing. Our approach may also be applied to analyse other types of peptide-centric structural proteomics data, such as FPOP or molecular painting data.
HostingRepository	PRIDE
AnnounceDate	2025-05-05
AnnouncementXML	Submission_2025-05-05_07:21:39.095.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Valentina Cappelletti
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2024-09-11 12:37:46	ID requested
⏵ 1	2025-05-05 07:21:39	announced

10.1016/J.MCPRO.2025.100934;

submitter keyword: S.cerevisiae,Yeast, DIA, LiP-MS, LC-MS/MS

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
Valentina Cappelletti
contact affiliation	ETH
contact email	cappelletti@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/2025/05/PXD055783

PRIDE project URI

• PRIDE
  1. PXD055783
     1. Label: PRIDE project
     2. Name: Analysis of limited proteolysis-coupled mass spectrometry data