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The recent 10\u2010year trajectory of single\u2010cell proteomics has opened a new biological dimension for studying disease. Mitochondrial diseases, with their pronounced cell\u2010to\u2010cell heterogeneity, are particularly, well\u2010suited to these methods. Here, we discuss how this approach can serve as an orthogonal functional layer for rare disease diagnostics. We trace the evolution of rare disease diagnostics from biochemical enzyme assays through genomics, transcriptomics, proteomics and metabolomics, highlighting incremental gains in diagnostic yield from individual omics layers and their integration. We discuss the limitations of bulk approaches in capturing the functional consequences of genetic perturbations, the new opportunities opened up by single\u2010cell measurements and how spatial single\u2010cell proteomics can further enrich the biological signal of affected cells in diagnostic tissues. We observe that the persisting diagnostic gap reflects not only technological limitations but, increasingly, challenges in data sharing and infrastructure as well as interpretive frameworks for functional molecular evidence. In this context, we consider opportunities for artificial intelligence and the ethical dimensions of single\u2010cell proteomics in rare disease diagnostics. Finally, we propose a single\u2010cell deep visual proteomics (scDVP) framework for clinical diagnostics of rare diseases with cell\u2010to\u2010cell variability, arguing that mitochondrial diseases are an ideal proof\u2010of\u2010concept.<\/jats:p>","DOI":"10.1002\/jimd.70236","type":"journal-article","created":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T06:37:12Z","timestamp":1787639832000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["From Single Cells to Diagnosis: Proteomics Technologies in the Multi\u2010Omics Landscape of Rare and Mitochondrial Diseases"],"prefix":"10.1002","volume":"49","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1831-0376","authenticated-orcid":false,"given":"Simon","family":"Wetzel","sequence":"first","affiliation":[{"name":"Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics Karolinska Institutet  Stockholm Sweden"},{"name":"Science for 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