{"entity": "researcher", "timestamp": "2026-10-12T21:34:55.294Z", "family": "Gstaiger", "given": "Matthias", "initials": "M", "orcid": "0000-0002-3245-3253", "affiliations": ["Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland. matthias.gstaiger@imsb.biol.ethz.ch."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/8370f12358274bb2a5a4cd524ae4f465.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/8370f12358274bb2a5a4cd524ae4f465"}}, "publications": [{"entity": "publication", "iuid": "4fb1dd6f5f864787baae2144e261cca4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4fb1dd6f5f864787baae2144e261cca4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4fb1dd6f5f864787baae2144e261cca4"}}, "title": "A tissue-specific atlas of protein-protein associations enables prioritization of candidate disease genes.", "authors": [{"family": "Laman Trip", "given": "Diederik S", "initials": "DS", "orcid": "0000-0001-6635-0626", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a30f1c008f82468c8ae1d8964d997067.json"}}, {"family": "van Oostrum", "given": "Marc", "initials": "M", "orcid": "0000-0001-8747-9787", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/141897b2c0e748a9abb86cdea8bd8614.json"}}, {"family": "Memon", "given": "Danish", "initials": "D"}, {"family": "Frommelt", "given": "Fabian", "initials": "F", "orcid": "0000-0003-3666-8005", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e71a93da1624a17bcbace26ba50c5a5.json"}}, {"family": "Baptista", "given": "Delora", "initials": "D"}, {"family": "Panneerselvam", "given": "Kalpana", "initials": "K", "orcid": "0000-0003-2534-198X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e2cfb623f9d74273a76b9d5ddc894129.json"}}, {"family": "Bradley", "given": "Glyn", "initials": "G"}, {"family": "Licata", "given": "Luana", "initials": "L", "orcid": "0000-0001-5084-9000", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dbfb64fa4d6a4c61b68d808a13e173b7.json"}}, {"family": "Hermjakob", "given": "Henning", "initials": "H", "orcid": "0000-0001-8479-0262", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ef7fa5ba29447fba798a69b305c0228.json"}}, {"family": "Orchard", "given": "Sandra", "initials": "S", "orcid": "0000-0002-8878-3972", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/869478a873ea4465ab43ecef5aee865c.json"}}, {"family": "Trynka", "given": "Gosia", "initials": "G", "orcid": "0000-0002-6955-9529", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/22558d9cbf844bf6bd0063c2dde6f513.json"}}, {"family": "McDonagh", "given": "Ellen M", "initials": "EM"}, {"family": "Fossati", "given": "Andrea", "initials": "A"}, {"family": "Aebersold", "given": "Ruedi", "initials": "R", "orcid": "0000-0002-9576-3267", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4aa50db862e94831b8cac04c4426daf1.json"}}, {"family": "Gstaiger", "given": "Matthias", "initials": "M", "orcid": "0000-0002-3245-3253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8370f12358274bb2a5a4cd524ae4f465.json"}}, {"family": "Wollscheid", "given": "Bernd", "initials": "B"}, {"family": "Beltrao", "given": "Pedro", "initials": "P", "orcid": "0000-0002-2724-7703", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/952eba119d2e4d4b89e14b294c5c6885.json"}}], "type": "journal article", "published": "2026-04-00", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "volume": "44", "issue": "4", "pages": "654-667", "issn-l": "1087-0156"}, "abstract": "Despite progress in mapping protein-protein interactions, their tissue specificity is understudied. Here, given that protein coabundance is predictive of functional association, we compiled and analyzed protein abundance data of 7,811 proteomic samples from 11 human tissues to produce an atlas of tissue-specific protein associations. We find that this method recapitulates known protein complexes and the larger structural organization of the cell. Interactions of stable protein complexes are well preserved across tissues, while cell-type-specific cellular structures, such as synaptic components, are found to represent a substantial driver of differences between tissues. Over 25% of associations are tissue specific, of which <7% are because of differences in gene expression. We validate protein associations for the brain through cofractionation experiments in synaptosomes, curation of brain-derived pulldown data and AlphaFold2 modeling. We also construct a network of brain interactions for schizophrenia-related genes, indicating that our approach can functionally prioritize candidate disease genes in loci linked to brain disorders.", "doi": "10.1038/s41587-025-02659-z", "pmid": "40316700", "labels": {"DDLS Fellow": "", "Andrea Fossati": ""}, "xrefs": [{"db": "pmc", "key": "PMC13090126"}, {"db": "pii", "key": "10.1038/s41587-025-02659-z"}], "notes": [], "created": "2026-08-20T08:59:34.792Z", "modified": "2026-09-23T09:05:32.445Z"}, {"entity": "publication", "iuid": "65da812e265149fba8d4c311774023e2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/65da812e265149fba8d4c311774023e2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/65da812e265149fba8d4c311774023e2"}}, "title": "An atlas of protein-protein associations of human tissues prioritizes candidate disease genes", "authors": [{"family": "Laman Trip", "given": "Diederik S", "initials": "DS"}, {"family": "van Oostrum", "given": "Marc", "initials": "M"}, {"family": "Memon", "given": "Danish", "initials": "D"}, {"family": "Frommelt", "given": "Fabian", "initials": "F", "orcid": "0000-0003-3666-8005", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e71a93da1624a17bcbace26ba50c5a5.json"}}, {"family": "Baptista", "given": "Delora", "initials": "D"}, {"family": "Panneerselvam", "given": "Kalpana", "initials": "K"}, {"family": "Bradley", "given": "Glyn", "initials": "G"}, {"family": "Licata", "given": "Luana", "initials": "L"}, {"family": "Hermjakob", "given": "Henning", "initials": "H", "orcid": "0000-0001-8479-0262", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ef7fa5ba29447fba798a69b305c0228.json"}}, {"family": "Orchard", "given": "Sandra", "initials": "S"}, {"family": "Trynka", "given": "Gosia", "initials": "G"}, {"family": "McDonagh", "given": "Ellen", "initials": "E"}, {"family": "Fossati", "given": "Andrea", "initials": "A", "orcid": "0000-0001-5170-4903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/658637b885384441943698722fad5944.json"}}, {"family": "Aebersold", "given": "Ruedi", "initials": "R", "orcid": "0000-0002-9576-3267", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4aa50db862e94831b8cac04c4426daf1.json"}}, {"family": "Gstaiger", "given": "Matthias", "initials": "M", "orcid": "0000-0002-3245-3253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8370f12358274bb2a5a4cd524ae4f465.json"}}, {"family": "Wollscheid", "given": "Bernd", "initials": "B", "orcid": "0000-0002-3923-1610", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fecd11050305473ca698ba6c6ee54a52.json"}}, {"family": "Beltrao", "given": "Pedro", "initials": "P", "orcid": "0000-0002-2724-7703", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/952eba119d2e4d4b89e14b294c5c6885.json"}}], "type": "posted-content", "published": "2024-05-17", "journal": {"title": null, "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2024.05.15.594301", "pmid": null, "labels": {"Andrea Fossati": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-18T16:51:07.686Z", "modified": "2025-03-21T13:32:48.505Z"}, {"entity": "publication", "iuid": "b44b20675f284acb911d497d1301f76c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b44b20675f284acb911d497d1301f76c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b44b20675f284acb911d497d1301f76c"}}, "title": "DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes.", "authors": [{"family": "Frommelt", "given": "Fabian", "initials": "F", "orcid": "0000-0003-3666-8005", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e71a93da1624a17bcbace26ba50c5a5.json"}}, {"family": "Fossati", "given": "Andrea", "initials": "A", "orcid": "0000-0001-5170-4903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/658637b885384441943698722fad5944.json"}}, {"family": "Uliana", "given": "Federico", "initials": "F"}, {"family": "Wendt", "given": "Fabian", "initials": "F", "orcid": "0000-0002-2501-536X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f9f0e10e0ff84bfdba2da72790f12c32.json"}}, {"family": "Xue", "given": "Peng", "initials": "P"}, {"family": "Heusel", "given": "Moritz", "initials": "M"}, {"family": "Wollscheid", "given": "Bernd", "initials": "B", "orcid": "0000-0002-3923-1610", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fecd11050305473ca698ba6c6ee54a52.json"}}, {"family": "Aebersold", "given": "Ruedi", "initials": "R", "orcid": "0000-0002-9576-3267", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4aa50db862e94831b8cac04c4426daf1.json"}}, {"family": "Ciuffa", "given": "Rodolfo", "initials": "R"}, {"family": "Gstaiger", "given": "Matthias", "initials": "M", "orcid": "0000-0002-3245-3253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8370f12358274bb2a5a4cd524ae4f465.json"}}], "type": "journal article", "published": "2024-04-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "issn-l": "1548-7091", "volume": "21", "issue": "4", "pages": "635-647"}, "abstract": "Most proteins are organized in macromolecular assemblies, which represent key functional units regulating and catalyzing most cellular processes. Affinity purification of the protein of interest combined with liquid chromatography coupled to tandem mass spectrometry (AP-MS) represents the method of choice to identify interacting proteins. The composition of complex isoforms concurrently present in the AP sample can, however, not be resolved from a single AP-MS experiment but requires computational inference from multiple time- and resource-intensive reciprocal AP-MS experiments. Here we introduce deep interactome profiling by mass spectrometry (DIP-MS), which combines AP with blue-native-PAGE separation, data-independent acquisition with mass spectrometry and deep-learning-based signal processing to resolve complex isoforms sharing the same bait protein in a single experiment. We applied DIP-MS to probe the organization of the human prefoldin family of complexes, resolving distinct prefoldin holo- and subcomplex variants, complex-complex interactions and complex isoforms with new subunits that were experimentally validated. Our results demonstrate that DIP-MS can reveal proteome modularity at unprecedented depth and resolution.", "doi": "10.1038/s41592-024-02211-y", "pmid": "38532014", "labels": {"Andrea Fossati": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11009110"}, {"db": "pii", "key": "10.1038/s41592-024-02211-y"}], "notes": [], "created": "2025-03-18T16:51:10.645Z", "modified": "2025-03-21T13:32:23.292Z"}]}