{"entity": "researcher", "timestamp": "2026-11-12T14:03:40.896Z", "family": "Federico", "given": "Uliana", "initials": "U", "orcid": "0000-0002-8185-6438", "affiliations": ["Johannes Gutenberg University of Mainz, Mainz, 55122, Germany."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/3f0d1d41912a480090caaf56d6b8c6c1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/3f0d1d41912a480090caaf56d6b8c6c1"}}, "publications": [{"entity": "publication", "iuid": "61b1ac7c6ef84fc58fb6ee80ff2e4ba7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/61b1ac7c6ef84fc58fb6ee80ff2e4ba7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/61b1ac7c6ef84fc58fb6ee80ff2e4ba7"}}, "title": "Need for speed: advances in the era of high throughput interaction proteomics.", "authors": [{"family": "Frommelt", "given": "Fabian", "initials": "F", "orcid": "0000-0003-3666-8005", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e71a93da1624a17bcbace26ba50c5a5.json"}}, {"family": "Federico", "given": "Uliana", "initials": "U", "orcid": "0000-0002-8185-6438", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3f0d1d41912a480090caaf56d6b8c6c1.json"}}, {"family": "Aebersold", "given": "Ruedi", "initials": "R", "orcid": "0000-0002-9576-3267", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4aa50db862e94831b8cac04c4426daf1.json"}}, {"family": "Fossati", "given": "Andrea", "initials": "A", "orcid": "0000-0001-5170-4903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/658637b885384441943698722fad5944.json"}}], "type": "journal article", "published": "2026-03-06", "journal": {"title": "Mol Omics", "issn": "2515-4184", "volume": "22", "issue": "2", "issn-l": null}, "abstract": "Protein-protein interactions are central to virtually all biological processes, forming intricate networks that operate in a highly regulated manner. These interactions are not permanent but rather continuously adapt to environmental changes, developmental cues, or disease-related stress. Understanding which protein interactions are present in a specific cellular state and how they adapt to specific stimuli is one of the long-standing goals of modern systems biology. Mass spectrometry (MS)-based proteomics has emerged as the primary tool for charting these networks. Over the past two decades, continuous advances in instrumentation, sample preparation, and data analysis have enabled researchers to explore the protein interaction landscape with increasing depth and accuracy. This has led to important discoveries in areas ranging from fundamental cell signalling to the identification of new therapeutic targets. We present the current state of MS-based protein interaction analysis, focusing on the three most widely utilized approaches: affinity purification, proximity labelling, and co-fractionation MS. For each, we discuss the fundamental approach, technical considerations, limitations, and highlight the potential integration with future technologies and datasets. Recent innovations such as short-gradient chromatography and faster data acquisition have further improved sensitivity and throughput. Together, these developments are bringing researchers closer to mapping the dynamic, context-dependent architecture of protein networks in unprecedented detail.", "doi": "10.1093/molecular-omics/aaiag012", "pmid": "41792901", "labels": {"Andrea Fossati": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "8509911"}], "notes": [], "created": "2026-11-06T07:58:49.985Z", "modified": "2026-11-06T07:58:50.125Z"}, {"entity": "publication", "iuid": "d96fcf3877f44b5cb7e4051643c516fe", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d96fcf3877f44b5cb7e4051643c516fe.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d96fcf3877f44b5cb7e4051643c516fe"}}, "title": "Phosphorylation-linked complex profiling identifies assemblies required for Hippo signal integration.", "authors": [{"family": "Uliana", "given": "Federico", "initials": "F", "orcid": "0000-0002-8185-6438", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3f0d1d41912a480090caaf56d6b8c6c1.json"}}, {"family": "Ciuffa", "given": "Rodolfo", "initials": "R"}, {"family": "Mishra", "given": "Ranjan", "initials": "R"}, {"family": "Fossati", "given": "Andrea", "initials": "A", "orcid": "0000-0001-5170-4903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/658637b885384441943698722fad5944.json"}}, {"family": "Frommelt", "given": "Fabian", "initials": "F"}, {"family": "Keller", "given": "Sabrina", "initials": "S", "orcid": "0000-0002-8976-9208", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0b11771587fa4fae82e5cf729a9f39d4.json"}}, {"family": "Mehnert", "given": "Martin", "initials": "M"}, {"family": "Birkeland", "given": "Eivind Salmorin", "initials": "ES"}, {"family": "van Drogen", "given": "Frank", "initials": "F"}, {"family": "Srejic", "given": "Nevena", "initials": "N", "orcid": "0000-0002-6568-4066", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/996636135e6942ae973c6971be6c0a03.json"}}, {"family": "Peter", "given": "Matthias", "initials": "M", "orcid": "0000-0002-2160-6824", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e25e09234cbf44779e8b94d8d8559867.json"}}, {"family": "Tapon", "given": "Nicolas", "initials": "N"}, {"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"}}], "type": "journal article", "published": "2023-04-12", "journal": {"title": "Mol Syst Biol", "issn": "1744-4292", "volume": "19", "issue": "4", "pages": "e11024", "issn-l": "1744-4292"}, "abstract": "While several computational methods have been developed to predict the functional relevance of phosphorylation sites, experimental analysis of the interdependency between protein phosphorylation and Protein-Protein Interactions (PPIs) remains challenging. Here, we describe an experimental strategy to establish interdependencies between protein phosphorylation and complex formation. This strategy is based on three main steps: (i) systematically charting the phosphorylation landscape of a target protein; (ii) assigning distinct proteoforms of the target protein to different protein complexes by native complex separation (AP-BNPAGE) and protein correlation profiling; and (iii) analyzing proteoforms and complexes in cells lacking regulators of the target protein. We applied this strategy to YAP1, a transcriptional co-activator for the control of organ size and tissue homeostasis that is highly phosphorylated and among the most connected proteins in human cells. We identified multiple YAP1 phosphosites associated with distinct complexes and inferred how both are controlled by Hippo pathway members. We detected a PTPN14/LATS1/YAP1 complex and suggest a model how PTPN14 inhibits YAP1 via augmenting WW domain-dependent complex formation and phosphorylation by LATS1/2.", "doi": "10.15252/msb.202211024", "pmid": "36896621", "labels": {"Andrea Fossati": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10090947"}], "notes": [], "created": "2026-11-06T08:03:11.318Z", "modified": "2026-11-06T08:03:11.587Z"}]}