{"entity": "researcher", "timestamp": "2026-09-23T16:50:05.300Z", "family": "Gharibi", "given": "Hassan", "initials": "H", "orcid": "0000-0002-3072-4929", "affiliations": ["Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/5825ec93851a42618425b67a5bbfbf3f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/5825ec93851a42618425b67a5bbfbf3f"}}, "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": "f65d016f0feb4d12b7a9dcf3e9918199", "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"}, {"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": "3ea25ac45a834483bdc7665a73b27f41", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3ea25ac45a834483bdc7665a73b27f41.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3ea25ac45a834483bdc7665a73b27f41"}}, "title": "Proteomics-Compatible Fourier Transform Isotopic Ratio Mass Spectrometry of Polypeptides.", "authors": [{"family": "Gharibi", "given": "Hassan", "initials": "H", "orcid": "0000-0002-3072-4929", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5825ec93851a42618425b67a5bbfbf3f.json"}}, {"family": "Chernobrovkin", "given": "Alexey L", "initials": "AL", "orcid": "0000-0001-7709-0161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/011675da8d7a4fd68fbe5ce03227978d.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"}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M", "orcid": "0000-0001-5610-0797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a402c63fbe4f478daa286177f031b923.json"}}, {"family": "Makarov", "given": "Alexander A", "initials": "AA", "orcid": "0000-0002-7046-6709", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/73e01f8c0f8641d894824a878ffcb8ff.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": "2022-11-01", "journal": {"title": "Anal. Chem.", "issn": "1520-6882", "volume": "94", "issue": "43", "pages": "15048-15056", "issn-l": "0003-2700"}, "abstract": "Measuring the relative abundances of heavy stable isotopes of the elements C, H, N, and O in proteins is of interest in environmental science, archeology, zoology, medicine, and other fields. The isotopic abundance measurements of the fine structure of immonium ions with ultrahigh resolution mass spectrometry obtained in gas-phase fragmentation of polypeptides have previously uncovered anomalous deuterium enrichment in (hydroxy)proline of bone collagen in marine mammals. Here, we provide a detailed description and validation of this approach and demonstrate per mil-range precision of isotopic ratio measurements in aliphatic residues from proteins and cell lysates. The analysis consists of proteomics-type experiment demanding sub-microgram amounts of a protein sample and providing concomitantly protein sequence data allowing one to verify sample purity and establish its identity. A novel software tool protein amino acid-resolved isotopic ratio mass spectrometry (PAIR-MS) is presented for extracting isotopic ratio data from the raw data files acquired on an Orbitrap mass spectrometer.", "doi": "10.1021/acs.analchem.2c03119", "pmid": "36251694", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9631351"}], "notes": [], "created": "2026-09-23T11:15:36.689Z", "modified": "2026-09-23T11:15:36.865Z"}, {"entity": "publication", "iuid": "c28fb876d1334187af97136f2fff26d0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c28fb876d1334187af97136f2fff26d0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c28fb876d1334187af97136f2fff26d0"}}, "title": "System-wide identification and prioritization of enzyme substrates by thermal analysis.", "authors": [{"family": "Saei", "given": "Amir Ata", "initials": "AA", "orcid": "0000-0002-2639-6328", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ebf703f0f2d44b14846ea1d9811b6e0d.json"}}, {"family": "Beusch", "given": "Christian M", "initials": "CM", "orcid": "0000-0001-9100-8283", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fbb4771768354080ab5292c96fee0812.json"}}, {"family": "Sabatier", "given": "Pierre", "initials": "P", "orcid": "0000-0002-2734-1791", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4cf83f2cf534d7eb308dab89d6460e2.json"}}, {"family": "Wells", "given": "Juan Astorga", "initials": "JA", "orcid": "0000-0003-1017-8841", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/855ef6e5db6f4791a52eeae9ffb95a30.json"}}, {"family": "Gharibi", "given": "Hassan", "initials": "H", "orcid": "0000-0002-3072-4929", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5825ec93851a42618425b67a5bbfbf3f.json"}}, {"family": "Meng", "given": "Zhaowei", "initials": "Z"}, {"family": "Chernobrovkin", "given": "Alexey", "initials": "A", "orcid": "0000-0001-7709-0161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/011675da8d7a4fd68fbe5ce03227978d.json"}}, {"family": "Rodin", "given": "Sergey", "initials": "S"}, {"family": "N\u00e4reoja", "given": "Katja", "initials": "K"}, {"family": "Thorsell", "given": "Ann-Gerd", "initials": "AG"}, {"family": "Karlberg", "given": "Tobias", "initials": "T"}, {"family": "Cheng", "given": "Qing", "initials": "Q"}, {"family": "Lundstr\u00f6m", "given": "Susanna L", "initials": "SL"}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M", "orcid": "0000-0001-5610-0797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a402c63fbe4f478daa286177f031b923.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": "Arn\u00e9r", "given": "Elias S J", "initials": "ESJ", "orcid": "0000-0002-4807-6114", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3502128dcae54dfcb6808356694bf4dc.json"}}, {"family": "Sch\u00fcler", "given": "Herwig", "initials": "H", "orcid": "0000-0003-4059-3501", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a66d04210ea41c2bbb0a5ee187c7b76.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": "2021-02-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "1296", "issn-l": "2041-1723"}, "abstract": "Despite the immense importance of enzyme-substrate reactions, there is a lack of general and unbiased tools for identifying and prioritizing substrate proteins that are modified by the enzyme on the structural level. Here we describe a high-throughput unbiased proteomics method called System-wide Identification and prioritization of Enzyme Substrates by Thermal Analysis (SIESTA). The approach assumes that the enzymatic post-translational modification of substrate proteins is likely to change their thermal stability. In our proof-of-concept studies, SIESTA successfully identifies several known and novel substrate candidates for selenoprotein thioredoxin reductase 1, protein kinase B (AKT1) and poly-(ADP-ribose) polymerase-10 systems. Wider application of SIESTA can enhance our understanding of the role of enzymes in homeostasis and disease, opening opportunities to investigate the effect of post-translational modifications on signal transduction and facilitate drug discovery.", "doi": "10.1038/s41467-021-21540-6", "pmid": "33637753", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7910609"}, {"db": "pii", "key": "10.1038/s41467-021-21540-6"}], "notes": [], "created": "2026-09-23T08:34:01.574Z", "modified": "2026-09-23T08:34:01.919Z"}]}