PXD049007

PXD049007 is an original dataset announced via ProteomeXchange.

Title	Gel-Assisted Proteome Position Integral Shift (GAPPIS) Assay Returns Molecular Weight to Shotgun Proteomics and Identifies Novel Caspase 3 Substrates
Description	Here we present a high-throughput virtual top-down proteomics approach that restores the molecular weight (MW) information in shotgun proteomics, and demonstrate its utility in studying proteolytic events in programmed cell death. With Gel-Assisted Proteome Position Integral Shift (GAPPIS), we quantified over 7000 proteins in staurosporine-induced apoptotic HeLa cells and identified 89 proteins exhibiting in a statistically significant manner at least two of the following features: 1) a negative MW shift; 2) an elevated ratio in a pair of a semi-tryptic and tryptic peptide, 3) a negative shift in the standard deviation of MW estimated for different peptides, and 4) a negative shift in skewness of the same data. Of these proteins, 60 molecules were novel caspase 3 substrates. Further analysis identified the preferred cleavage sites consistent with the known caspase cleavages after the DXXD motif. As a powerful tool for high-throughput MW analysis simultaneously with the conventional expression analysis, GAPPIS assay can prove useful in studying a broad range of biological processes involving proteolytic activity.
HostingRepository	PRIDE
AnnounceDate	2025-03-11
AnnouncementXML	Submission_2025-03-11_07:14:36.989.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Zhaowei Meng
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF; Orbitrap Fusion Lumos; Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-01-30 06:18:51	ID requested
⏵ 1	2025-03-11 07:14:37	announced

10.1021/acs.analchem.4c02051;

Meng Z, Saei AA, Gharibi H, Zhang X, Lyu H, Lundstr, ö, m SL, V, é, gv, á, ri Á, Gaetani M, Zubarev RA, Gel-Assisted Proteome Position Integral Shift Assay Returns Molecular Weight to Shotgun Proteomics and Identifies Caspase 3 Substrates. Anal Chem, 96(33):13533-13541(2024) [pubmed]

submitter keyword: Molecular Weight，Shotgun Proteomics，mass spectrometry, caspase 3,gel electrophoresis

Roman A. Zubarev
contact affiliation	Department of Medical Biophysics and Biochemistry, Karolinska Institutet
contact email	roman.zubarev@ki.se
lab head
Zhaowei Meng
contact affiliation	Department of Medical Biophysics and Biochemistry, Karolinska Institutet
contact email	zhaowei.meng@ki.se
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/2025/03/PXD049007

PRIDE project URI

• PRIDE
  1. PXD049007
     1. Label: PRIDE project
     2. Name: Gel-Assisted Proteome Position Integral Shift (GAPPIS) Assay Returns Molecular Weight to Shotgun Proteomics and Identifies Novel Caspase 3 Substrates