The PRIDE Affinity-Proteomics Archive (PRIDE-AP): Making Affinity Proteomics Data FAIR

High-throughput affinity proteomics (AP) technologies, such as Olink and SomaScan, are central to biomarker discovery and clinical studies, but unlike mass spectrometry (MS)-based proteomics, they have lacked a dedicated, standards-driven open-data repository. To address this gap, we introduce the PRIDE Affinity Proteomics Archive (PRIDE-AP), a centralized, open, technology-agnostic repository extending the PRIDE infrastructure to support submission, storage, and reuse of AP datasets in compliance with FAIR principles. Each dataset receives a stable PAD identifier and DOI and undergoes automated validation. We extended the HUPO-PSI SDRF-Proteomics format and the PRIDE controlled vocabulary for AP experiments, and integrated quality-control statistics via the open-source library pyprideap. As of May 2026, PRIDE-AP includes 20 public datasets spanning 14 human diseases, with evidence for over 10,000 proteins. By enabling AP and MS datasets to be jointly deposited and linked, with protein-centric exploration cross-referenced to UniProt, PRIDE-AP enables cross-technology proteome interrogation at scale.