Deepti Kundu (Cambridge / GB), Selvakumar Kamatchinathan (Cambridge / GB), Chakradhar Bandla (Cambridge / GB), Jingwen Bai (Cambridge / GB), Suresh Hewapathirana (Cambridge / GB), Kathy Nevola (Uppsala / SE), Lina Hultin Rosenberg (Uppsala / SE), Eva Schmidt (Uppsala / SE), Juan Vizcaino (Cambridge / GB), Yasset Perez Riverol (Cambridge / GB)
Background
The PRIDE database at the European Bioinformatics Institute, also a founder of ProteomeXchange, is the most popular resource supporting open science practices in the mass spectrometry-based proteomics field. The PRIDE Affinity Proteomics (PRIDE-AP) Archive, is a new dedicated section within PRIDE that aims to revolutionize affinity proteomics by centralizing openly accessible datasets generated using affinity proteomics platforms. PRIDE-AP Archive aims to establish an inclusive technology-agnostic repository representing all companies. As a first step, data submission of Olink Proteomics Proximity Extension Assay (PEA) (https://olink.com/) has been realized. By adhering to the principles of Findability, Accessibility, Interoperability, and Reusability (FAIR), PRIDE-AP seeks to enhance collaboration, expedite research, and ensure the high-quality dissemination of affinity proteomics data.
Methods
The PRIDE-AP Archive defines a set of guidelines for the submission, validation and dissemination of affinity proteomics datasets while maintaining stringent adherence to FAIR principles. PRIDE-AP employs a robust submission (using the PRIDE submission tool) and validation process to ensure datasets meet comprehensive metadata and file requirements. Each dataset is assigned a unique PAD identifier (e.g., PAD000001) for citation. Submitters must provide essential metadata, including title, description, sample and data analysis protocols, and information on data submitters and principal investigators. Currently supported technologies include Olink Proteomics (e.g. Explore & Target technologies) submissions with their specific 'RAW' file type requirements (.parquet for Olink Proteomics). Additional files, such as experimental design documents and quality control reports, can also be included. The PRIDE-AP Archive infrastructure facilitates data submission, review, and public release, and the data remains unreleased to the public until publication.
Results and Discussion
Since its inception, PRIDE-AP has successfully integrated several high-quality affinity proteomics datasets, making them accessible to the scientific community. Implementing unique PAD identifiers has streamlined dataset citation and potential reuse in the scientific literature. The structured metadata requirements and stringent file validation processes have resulted in well-annotated, interoperable datasets. The PRIDE-AP Archive significantly advances the field of affinity proteomics by adhering to the FAIR principles. By centralizing datasets from technologies such as Olink Proteomics, PRIDE-AP facilitates collaboration, accelerates research, and promotes the widespread dissemination of high-quality data. Moving forward, PRIDE-AP will evolve, supporting new technologies and expanding its impact on the affinity proteomics field.