Press Release Issued on Promoting Data Reuse by Linking Repositories and Data Journals in jPOST

On Dec. 13, 2024 , Niigata University and Kyoto University issued a press release announcing that Japan Proteome Standard Repository/Database (jPOST) , an integrated database of proteome data, has established a system to facilitate the reanalysis of proteome data. In this press release, they introduced the launch of a data journal to collect detailed metadata required for data reanalysis (e.g., sample origin information, pretreatment and measurement conditions) and the development of their own quality evaluation index for experimental data, which is important for reanalysis, and described that jPOST is expected to contribute to the promotion of proteome data reanalysis research and open science in accordance with the FAIR Principles (*) through these efforts. The details are described in an article published in the Database Issue of the scientific journal Nucleic Acids Research on Dec. 11, 2024.

jPOST consists of 1) "jPOSTrepo", a repository of proteome mass spectrometry data, 2) a proteome raw data reanalysis system based on standardized protocols, and 3) "jPOSTdb", a database integrating the reanalysis data.

In recent years, advances in mass spectrometry have facilitated the acquisition of precise proteome data, and proteomics research has been widely conducted in various research fields, and many research data have been made available through public databases. On the other hand, while there are technical situations unique to mass spectrometry, where data cannot be compared and analyzed unless sample pretreatment and measurement conditions are consistent, sufficient metadata necessary for reanalysis is often not registered, and there are no appropriate quality evaluation indicators for experimental data, which is important for reanalysis. The press release states that this is one of the reasons why the reuse of proteome experimental data has not progressed well.

To address the above issues, jPOST, in collaboration with the Proteomics Society of Japan, has launched the Journal of Proteome Data and Methods (JPDM) in 2019, a data journal to detail accurate and detailed metadata (sample origin information, pretreatment and measurement conditions, etc.) required for data re-analysis. In addition, they have developed a original index, the UniScore, which evaluates the quality of each experimental data. A preprint paper on UniScore was published in BioRxiv in Oct. 2024. jPOST is currently evaluating the quality of registered data in jPOSTrepo using UniScore, and then reanalyzing the data based on metadata in JPDM articles, and publishing the results from jPOSTdb. As of Nov 2024 , 3,077 records have been registered in jPOSTrepo, of which 2,318 have been published, and 847 reanalysis data have been published in jPOSTdb.

For details, please see the press release from Niigata University and Kyoto University and the article "jPOST environment accelerates the reuse and reanalysis of public proteome mass spectrometry data" .

jPOST is developed as a part of JST Database Integration Coordination Program (DICP), "jPOST prime: proteome database environment based on community cooperation" (Principal Investigater: ISHIHAMA Yasushi, Professor, Graduate School of Pharmaceutical Sciences, Kyoto University).

*FAIR Principles: Guidelines that outline principles for making data "Findable," "Accessible," "Interoperable," and "Reusable."