PXD049007 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2024-01-30 06:18:51 | ID requested | |
⏵ 1 | 2025-03-11 07:14:37 | announced | |
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 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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD049007
- Label: PRIDE project
- Name: Gel-Assisted Proteome Position Integral Shift (GAPPIS) Assay Returns Molecular Weight to Shotgun Proteomics and Identifies Novel Caspase 3 Substrates