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PXD049007

PXD049007 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleGel-Assisted Proteome Position Integral Shift (GAPPIS) Assay Returns Molecular Weight to Shotgun Proteomics and Identifies Novel Caspase 3 Substrates
DescriptionHere 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.
HostingRepositoryPRIDE
AnnounceDate2025-03-11
AnnouncementXMLSubmission_2025-03-11_07:14:36.989.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterZhaowei Meng
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListacetylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
InstrumentQ Exactive HF; Orbitrap Fusion Lumos; Orbitrap Exploris 480
Dataset History
RevisionDatetimeStatusChangeLog Entry
02024-01-30 06:18:51ID requested
12025-03-11 07:14:37announced
Publication List
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]
Keyword List
submitter keyword: Molecular Weight,Shotgun Proteomics,mass spectrometry, caspase 3,gel electrophoresis
Contact List
Roman A. Zubarev
contact affiliationDepartment of Medical Biophysics and Biochemistry, Karolinska Institutet
contact emailroman.zubarev@ki.se
lab head
Zhaowei Meng
contact affiliationDepartment of Medical Biophysics and Biochemistry, Karolinska Institutet
contact emailzhaowei.meng@ki.se
dataset submitter
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