Elaine Holmes

Proteomics is evolving. Researchers are increasingly conducting experiments that focus on health-related topics, which naturally involve patient samples. This shift necessitates greater attention to privacy, particularly in compliance with strict laws governing patient data.

A key expectation is that patient data be deidentified and appropriately protected. More frequently, such data is being stored in controlled-access repositories. At *JPR*, we have long upheld high standards for data transparency and expect data to be made available through repositories not controlled by the authors. By and large, this system has worked well, as robust repositories exist for proteomic and metabolomic data.

However, we have observed a growing trend of studies generating patient data, both by mass spectrometry and affinity proteomics methods, and placing it into controlled-access repositories. We note that the PRIDE database, which is a member of the ProteomeXchange Consortium, now accepts submissions of Olink and SomaLogic data in both their open and controlled-access repositories.

While we remain committed to the principle of universal data availability, we acknowledge that tracking who gains access to sensitive data is a reasonable requirement. In response to these developments, we have therefore updated our data transparency policy to better align with privacy regulations. We will now accept data deposits in controlled-access repositories─but not in limited-access repositories. Importantly, we expect all data to adhere to the FAIR principles of being findable, accessible, interoperable and reusable. While FAIR does not mean the data itself is open, the (nonsensitive) metadata about the data should be─ideally in a machine-readable format such as SDRF [10.1038/s41467-021-26111-3]. For controlled-access data, we expect it is also clearly describe how to request access to the data, e.g. through a data access committee or DAC, in accordance with applicable regulations and the study subject informed consent. This expectation holds for proteomics as well as metabolomics data, regardless of the repository or experimental method, recognizing that mass spectrometry proteomics data is particularly sensitive as it can be personally identifiable by itself [10.1016/j.mcpro.2021.100071]. Papers should include how people can access the data giving the location of the data, the accession number, and whether it is open or controlled access. This information will help people access the data to provide full transparency.

The *JPR* data transparency policy balances openness and privacy for proteomics and metabolomics data following the FAIR principles. Metadata should remain openly accessible, facilitating responsible data sharing while safeguarding sensitive personal information, thereby maximizing opportunities for data integration and reuse, and accelerating scientific discovery.