Standardized Annotation of Quantitative Proteomics Datasets Using SDRF-Proteomics

Proteomics datasets require detailed and standardized metadata annotation to ensure reproducibility, reusability, and alignment with FAIR (Findable, Accessible, Interoperable, Reusable) principles. This chapter presents a practical, hands-on workflow for annotating a label-free proteomics dataset using the Sample and Data Relationship Format for Proteomics (SDRF-Proteomics), a HUPO-PSI and EuBIC-MS standard that has been adopted by major proteomics data repositories. We demonstrate the process on a COVID-19 nasal-swab dataset (PXD020394), showing how to derive sample and assay metadata from the study files, encode them in SDRF with the lesSDRF web application, and validate the result. Although the worked example is label-free, the approach can be generalized to other quantification strategies.