{"entity": "researcher", "timestamp": "2026-09-23T16:43:18.772Z", "family": "Meng", "given": "Zhaowei", "initials": "Z", "orcid": "0000-0002-7721-2795", "affiliations": ["Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden.", "Chemical Proteomics Unit, Science for Life Laboratory (SciLifeLab), 17165 Stockholm, Sweden.", "Chemical Proteomics, Swedish National Infrastructure for Biological Mass Spectrometry (BioMS), 17177 Stockholm, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/39ee47850dd643bbbc22d54f8e5419a3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/39ee47850dd643bbbc22d54f8e5419a3"}}, "publications": [{"entity": "publication", "iuid": "14e87800c7b848769642652462d73f6a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/14e87800c7b848769642652462d73f6a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/14e87800c7b848769642652462d73f6a"}}, "title": "Toward a Species Search Engine: KISSE Offers a Rigorous Statistical Framework for Bone Collagen Tandem Mass Spectrometry Data.", "authors": [{"family": "Gharibi", "given": "Hassan", "initials": "H", "orcid": "0000-0002-3072-4929", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5825ec93851a42618425b67a5bbfbf3f.json"}}, {"family": "Saei", "given": "Amir Ata", "initials": "AA", "orcid": "0000-0002-2639-6328", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ebf703f0f2d44b14846ea1d9811b6e0d.json"}}, {"family": "Chernobrovkin", "given": "Alexey L", "initials": "AL"}, {"family": "Lundstrom", "given": "Susanna L", "initials": "SL"}, {"family": "Lyu", "given": "Hezheng", "initials": "H", "orcid": "0009-0008-7995-6473", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ae4b8890f5d64b6b87d71ef5964e4747.json"}}, {"family": "Meng", "given": "Zhaowei", "initials": "Z", "orcid": "0000-0002-7721-2795", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/39ee47850dd643bbbc22d54f8e5419a3.json"}}, {"family": "Vegvari", "given": "Akos", "initials": "A", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/724d65ef088147c4988093b2b6b5f318.json"}}, {"family": "Gaetani", "given": "Massimilliano", "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": "2025-10-00", "journal": {"title": "Adv Sci (Weinh)", "issn": "2198-3844", "volume": "12", "issue": "40", "pages": "e03963", "issn-l": null}, "abstract": "DNA and bone collagen are two key sources of resilient molecular markers used to identify species from their remains. Collagen is more stable than DNA, and thus it is preferred for ancient and degraded samples. Current mass spectrometry-based collagen sequencing approaches are empirical and lack a rigorous statistical framework. Based on the well-developed approaches to protein identification in shotgun proteomics, a first approximation of the species search engine (SSE) is introduced. SSE named KISSE is based on a species-specific library of collagenous peptides that uses both peptide sequences and their relative abundances. The developed statistical model can identify the species and the probability of correct identification, as well as determine the likelihood of the analyzed species not being in the library. The advantages and limitations of the proposed approach, and the possibility of extending it to other tissues is discussed.", "doi": "10.1002/advs.202503963", "pmid": "40787835", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12561455"}], "notes": [], "created": "2026-09-23T15:49:58.614Z", "modified": "2026-09-23T15:49:58.662Z"}, {"entity": "publication", "iuid": "4b0e44bdbf9c4c1ca7fc7d6448bce1c8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4b0e44bdbf9c4c1ca7fc7d6448bce1c8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4b0e44bdbf9c4c1ca7fc7d6448bce1c8"}}, "title": "One-Pot Time-Induced Proteome Integral Solubility Alteration Assay for Automated and Sensitive Drug-Target Identification.", "authors": [{"family": "Meng", "given": "Zhaowei", "initials": "Z", "orcid": "0000-0002-7721-2795", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/39ee47850dd643bbbc22d54f8e5419a3.json"}}, {"family": "Saei", "given": "Amir Ata", "initials": "AA"}, {"family": "Lyu", "given": "Hezheng", "initials": "H"}, {"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": "2024-12-03", "journal": {"title": "Anal. Chem.", "issn": "1520-6882", "volume": "96", "issue": "48", "pages": "18917-18921", "issn-l": "0003-2700"}, "abstract": "The proteome integral solubility alteration (PISA) assay is widely used for identifying drug targets, but it is labor-intensive and time-consuming and requires a substantial amount of biological sample. Aiming at enabling automation and greatly reducing the sample amount, we developed one-pot time-induced (OPTI)-PISA. Here, we demonstrate OPTI-PISA performance on identifying targets of multiple drugs in cell lysate and scaling down the sample amount to sub-microgram levels, making the PISA method suitable for NanoProteomics. OPTI-PISA can be implemented using only the standard equipment of a proteomics lab.", "doi": "10.1021/acs.analchem.4c05127", "pmid": "39567183", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11618734"}], "notes": [], "created": "2026-09-23T11:30:10.156Z", "modified": "2026-09-23T11:30:10.241Z"}, {"entity": "publication", "iuid": "37ca151f203c41f5aab354a0237757f9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/37ca151f203c41f5aab354a0237757f9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/37ca151f203c41f5aab354a0237757f9"}}, "title": "One-Pot Time-Induced Proteome Integral Solubility Alteration (OPTI-PISA) assay for automated and sensitive drug target identification", "authors": [{"family": "Meng", "given": "Zhaowei", "initials": "Z", "orcid": "0000-0002-7721-2795", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/39ee47850dd643bbbc22d54f8e5419a3.json"}}, {"family": "Saei", "given": "Amir Ata", "initials": "AA", "orcid": "0000-0002-2639-6328", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ebf703f0f2d44b14846ea1d9811b6e0d.json"}}, {"family": "Lyu", "given": "Hezheng", "initials": "H", "orcid": "0009-0008-7995-6473", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ae4b8890f5d64b6b87d71ef5964e4747.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": "posted-content", "published": "2024-08-13", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.08.13.607299", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-09-23T15:40:32.118Z", "modified": "2026-09-23T15:40:32.185Z"}, {"entity": "publication", "iuid": "091d3c108f5647cb844899639a684b28", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/091d3c108f5647cb844899639a684b28.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/091d3c108f5647cb844899639a684b28"}}, "title": "ThermoTargetMiner as a proteome integral solubility alteration target database for prospective drugs against lung cancer", "authors": [{"family": "Lyu", "given": "Hezheng", "initials": "H", "orcid": "0009-0008-7995-6473", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ae4b8890f5d64b6b87d71ef5964e4747.json"}}, {"family": "Gharibi", "given": "Hassan", "initials": "H", "orcid": "0000-0002-3072-4929", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5825ec93851a42618425b67a5bbfbf3f.json"}}, {"family": "Sokolova", "given": "Bohdana", "initials": "B", "orcid": "0000-0003-3751-7129", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a3d5d8171f0a45aa978347675ab9f6fb.json"}}, {"family": "Varli", "given": "M\u00fccahit", "initials": "M"}, {"family": "Voiland", "given": "Anna", "initials": "A"}, {"family": "Nilsson", "given": "Brady", "initials": "B", "orcid": "0000-0003-2936-3035", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fb4d988df1a14be58ab1bea590713d0a.json"}}, {"family": "Meng", "given": "Zhaowei", "initials": "Z", "orcid": "0000-0002-7721-2795", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/39ee47850dd643bbbc22d54f8e5419a3.json"}}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M", "orcid": "0000-0001-5610-0797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a402c63fbe4f478daa286177f031b923.json"}}, {"family": "Saei", "given": "Amir Ata", "initials": "AA", "orcid": "0000-0002-2639-6328", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ebf703f0f2d44b14846ea1d9811b6e0d.json"}}, {"family": "Zubarev", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5e3f9910c1ff434c8056bdecf537e9ef.json"}}], "type": "posted-content", "published": "2024-08-06", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.08.06.606599", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-09-23T14:37:24.456Z", "modified": "2026-09-23T14:37:24.716Z"}, {"entity": "publication", "iuid": "451a6bf85dc54832b2d945e75ac4a627", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/451a6bf85dc54832b2d945e75ac4a627.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/451a6bf85dc54832b2d945e75ac4a627"}}, "title": "Gel-Assisted Proteome Position Integral Shift (GAPPIS) Assay Returns Molecular Weight to Shotgun Proteomics and Identifies Novel Caspase 3 Substrates", "authors": [{"family": "Meng", "given": "Zhaowei", "initials": "Z", "orcid": "0000-0002-7721-2795", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/39ee47850dd643bbbc22d54f8e5419a3.json"}}, {"family": "Saei", "given": "Amir Ata", "initials": "AA", "orcid": "0000-0002-2639-6328", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ebf703f0f2d44b14846ea1d9811b6e0d.json"}}, {"family": "Zhang", "given": "Xuepei", "initials": "X", "orcid": "0000-0001-8304-8437", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4dca931b482e41c8923ecc6fa0ae8ddf.json"}}, {"family": "Lyu", "given": "Hezheng", "initials": "H"}, {"family": "Gharibi", "given": "Hassan", "initials": "H", "orcid": "0000-0002-3072-4929", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5825ec93851a42618425b67a5bbfbf3f.json"}}, {"family": "Lundstr\u00f6m", "given": "Susanna L", "initials": "SL", "orcid": "0000-0003-2363-4287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e31204e8fca04d4ebfb45782bea1214b.json"}}, {"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": "posted-content", "published": "2024-02-15", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.02.14.579877", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-09-23T15:32:02.795Z", "modified": "2026-09-23T15:32:02.880Z"}, {"entity": "publication", "iuid": "13d75815a3a84344b2331e40d6d59edc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/13d75815a3a84344b2331e40d6d59edc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/13d75815a3a84344b2331e40d6d59edc"}}, "title": "System-wide profiling by proteome integral solubility alteration assay of drug residence times for target characterization", "authors": [{"family": "Sabatier", "given": "Pierre", "initials": "P", "orcid": "0000-0002-2734-1791", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4cf83f2cf534d7eb308dab89d6460e2.json"}}, {"family": "Beusch", "given": "Christian M", "initials": "CM", "orcid": "0000-0001-9100-8283", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fbb4771768354080ab5292c96fee0812.json"}}, {"family": "Meng", "given": "Zhaowei", "initials": "Z", "orcid": "0000-0002-7721-2795", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/39ee47850dd643bbbc22d54f8e5419a3.json"}}, {"family": "Zubarev", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5e3f9910c1ff434c8056bdecf537e9ef.json"}}], "type": "posted-content", "published": "2022-06-27", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.06.27.497697", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-09-23T15:19:12.937Z", "modified": "2026-09-23T15:19:12.966Z"}]}