{"entity": "publication", "iuid": "f65d016f0feb4d12b7a9dcf3e9918199", "timestamp": "2026-09-23T16:57:02.336Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f65d016f0feb4d12b7a9dcf3e9918199.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f65d016f0feb4d12b7a9dcf3e9918199"}}, "title": "Gel-Assisted Proteome Position Integral Shift Assay Returns Molecular Weight to Shotgun Proteomics and Identifies Caspase 3 Substrates.", "authors": [{"family": "Meng", "given": "Zhaowei", "initials": "Z"}, {"family": "Saei", "given": "Amir Ata", "initials": "AA", "orcid": "0000-0002-2639-6328", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ebf703f0f2d44b14846ea1d9811b6e0d.json"}}, {"family": "Gharibi", "given": "Hassan", "initials": "H", "orcid": "0000-0002-3072-4929", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5825ec93851a42618425b67a5bbfbf3f.json"}}, {"family": "Zhang", "given": "Xuepei", "initials": "X"}, {"family": "Lyu", "given": "Hezheng", "initials": "H"}, {"family": "Lundstr\u00f6m", "given": "Susanna L", "initials": "SL"}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/724d65ef088147c4988093b2b6b5f318.json"}}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M", "orcid": "0000-0001-5610-0797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a402c63fbe4f478daa286177f031b923.json"}}, {"family": "Zubarev", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5e3f9910c1ff434c8056bdecf537e9ef.json"}}], "type": "journal article", "published": "2024-08-20", "journal": {"title": "Anal. Chem.", "issn": "1520-6882", "volume": "96", "issue": "33", "pages": "13533-13541", "issn-l": "0003-2700"}, "abstract": "Here, we present a high-throughput virtual top-down proteomics approach that restores the molecular weight (MW) information in shotgun proteomics and demonstrates 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 84 proteins exhibiting in a statistically significant manner at least two of the following features: (i) a negative MW shift; (ii) an elevated ratio in a pair of a semitryptic and tryptic peptide, (iii) a negative shift in the standard deviation of MW estimated for different peptides, and (iv) a negative shift in skewness of the same data. Of these proteins, 58 molecules were previously unreported 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, the GAPPIS assay can prove useful in studying a broad range of biological processes involving proteolytic events.", "doi": "10.1021/acs.analchem.4c02051", "pmid": "39110629", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11339726"}], "notes": [], "created": "2026-09-23T13:20:19.996Z", "modified": "2026-09-23T13:20:20.035Z"}