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Understanding the substances\u2019 mode-of-action is crucial to develop alternative test strategies. Omics methods are promising tools to achieve this goal. Until now, most attention was focused on transcriptomics, while proteomics is not yet routinely applied in toxicology despite the large number of datasets available in public repositories. Exploiting the full potential of these datasets is hampered by differences in measurement procedures and follow-up data processing. Here we present the tool PROTEOMAS, which allows meta-analysis of proteomic data from public origin. The workflow was designed for analyzing proteomic studies in a harmonized way and to ensure transparency in the analysis of proteomic data for regulatory purposes. It agrees with the Omics Reporting Framework guidelines of the OECD with the intention to integrate proteomics to other omic methods in regulatory toxicology. The overarching aim is to contribute to\u00a0the development of AOPs and to understand the mode of action of substances. To demonstrate the robustness and reliability of our workflow we compared our results to those of the original studies. As a case study, we performed a meta-analysis of 25 proteomic datasets to investigate the toxicological effects of nanomaterials at the lung level. PROTEOMAS is an important contribution to the development of alternative test strategies enabling robust meta-analysis of proteomic data. This workflow commits to the FAIR principles (Findable, Accessible, Interoperable and Reusable) of computational protocols.<\/jats:p>","DOI":"10.1186\/s13321-023-00710-2","type":"journal-article","created":{"date-parts":[[2023,3,19]],"date-time":"2023-03-19T15:02:23Z","timestamp":1679238143000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["PROTEOMAS: a workflow enabling harmonized proteomic meta-analysis and proteomic signature mapping"],"prefix":"10.1186","volume":"15","author":[{"given":"Aileen","family":"Bahl","sequence":"first","affiliation":[]},{"given":"Celine","family":"Ibrahim","sequence":"additional","affiliation":[]},{"given":"Kristina","family":"Plate","sequence":"additional","affiliation":[]},{"given":"Andrea","family":"Haase","sequence":"additional","affiliation":[]},{"given":"J\u00f6rn","family":"Dengjel","sequence":"additional","affiliation":[]},{"given":"Penny","family":"Nymark","sequence":"additional","affiliation":[]},{"given":"Ver\u00f3nica I.","family":"Dumit","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,3,19]]},"reference":[{"key":"710_CR1","doi-asserted-by":"publisher","unstructured":"OECD (2018) Users' Handbook supplement to the Guidance Document for developing and assessing Adverse Outcome Pathways. https:\/\/doi.org\/10.1787\/5jlv1m9d1g32-en","DOI":"10.1787\/5jlv1m9d1g32-en"},{"key":"710_CR2","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1186\/s12989-020-00344-4","volume":"17","author":"S Halappanavar","year":"2020","unstructured":"Halappanavar S et al (2020) Adverse outcome pathways as a tool for the design of testing strategies to support the safety assessment of emerging advanced materials at the nanoscale. 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