PXD031627-2

PXD031627 is an original dataset announced via ProteomeXchange.

Title	Proteome-wide structural changes measured with limited proteolysis-mass spectrometry: an advanced protocol for high-throughput applications.
Description	Proteins regulate biological processes by changing their structure or abundance to accomplish a specific function. In response to any perturbation or stimulus, protein structure may be altered by a variety of molecular events, such as post translational modification, protein-protein interaction, aggregation, allostery, or binding to other molecules. The ability to probe these structural changes in thousands of proteins simultaneously in cells or tissues can provide valuable information about the functional state of a variety of biological processes and pathways. Here we present an updated protocol for LiP-MS, a proteomics technique combining limited proteolysis with mass spectrometry, to detect protein structural alterations in complex backgrounds and on a proteome-wide scale (Cappelletti et al., 2021; Piazza et al., 2020; Schopper et al., 2017). We describe advances in the throughput and robustness of the LiP-MS workflow and implementation of data-independent acquisition (DIA) based mass spectrometry, which together achieve high reproducibility and sensitivity, even on large sample sizes. In addition, we introduce MSstatsLiP, an R package dedicated to the analysis of LiP-MS data for the identification of structurally altered peptides and differentially abundant proteins. Altogether, the newly proposed improvements expand the adaptability of the method and allow for its wide use in systematic functional proteomic studies and translational applications.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:55:53.606.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	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-02-11 06:39:56	ID requested
1	2023-01-10 04:48:57	announced
⏵ 2	2023-11-14 08:55:54	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: alpha-synuclein, shotgun proteomics, yeast, structural proteomics,LiP-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/2023/01/PXD031627

PRIDE project URI

• PRIDE
  1. PXD031627
     1. Label: PRIDE project
     2. Name: Proteome-wide structural changes measured with limited proteolysis-mass spectrometry: an advanced protocol for high-throughput applications.