biostudies-literatureUnknown16(1)Viegener WMetadata plays an essential role in the analysis and dissemination of proteomics data. It annotates sample information for output tables from library searches and displays sample information from data files in public repositories. However, integrating metadata into data analysis can be time-consuming and is not well standardized. Inconsistent metadata formats in public repositories hinder other researchers' ability to reproduce and reuse these public datasets. Here we present the metadata integration in MaxQuant, which provides a user-friendly way to export metadata as SDRF, the standard format that maps sample properties to proteomics data files. We also implemented the annotation of output tables with the SDRF file, enabling users to perform seamless downstream data analysis with annotatNature communications8421https://www.ebi.ac.uk/biostudies/studies/S-EPMC12462489biostudies-literatureFacilitating analysis and dissemination of proteomics data through metadata integration in MaxQuant.PMC12462489Cox JFerretti DUrazbakhtin SXiao JViegener WfalseFacilitating analysis and dissemination of proteomics data through metadata integration in MaxQuant.Metadata plays an essential role in the analysis and dissemination of proteomics data. It annotates sample information for output tables from library searches and displays sample information from data files in public repositories. However, integrating metadata into data analysis can be time-consuming and is not well standardized. Inconsistent metadata formats in public repositories hinder other researchers' ability to reproduce and reuse these public datasets. Here we present the metadata integration in MaxQuant, which provides a user-friendly way to export metadata as SDRF, the standard format that maps sample properties to proteomics data files. We also implemented the annotation of output tables with the SDRF file, enabling users to perform seamless downstream data analysis with annotat2025-01-01T00:00:00Z2025 Sep2026-06-03T20:27:43.971Z2026-06-01T03:06:16.031ZS-EPMC124624894099883210.1038/s41467-025-64089-4