Proteomic repository data submission, dissemination, and reuse: key messages

ABSTRACT

Introduction

The creation of ProteomeXchange data workflows in 2012 transformed the field of proteomics, consisting of the standardization of data submission and dissemination and enabling the widespread reanalysis of public MS proteomics data worldwide. ProteomeXchange has triggered a growing trend toward public dissemination of proteomics data, facilitating the assessment, reuse, comparative analyses, and extraction of new findings from public datasets. By 2022, the consortium is integrated by PRIDE, PeptideAtlas, MassIVE, jPOST, iProX, and Panorama Public.

Areas covered

Here, we review and discuss the current ecosystem of resources, guidelines, and file formats for proteomics data dissemination and reanalysis. Special attention is drawn to new exciting quantitative and post-translational modification-oriented resources. The challenges and future directions on data depositions including the lack of metadata and cloud-based and high-performance software solutions for fast and reproducible reanalysis of the available data are discussed.

Expert opinion

The success of ProteomeXchange and the amount of proteomics data available in the public domain have triggered the creation and/or growth of other protein knowledgebase resources. Data reuse is a leading, active, and evolving field; supporting the creation of new formats, tools, and workflows to rediscover and reshape the public proteomics data.

KEYWORDS:

• Proteomics databases
• public proteomics data
• protein expression
• standard file formats
• data reuse and reanalysis
• proteomics
• mass spectrometry
• computational biology
• open access data
• data integration

Acknowledgments

I would like to thank Lennart Martens’ team, Eric Deutsch, and Ronald Beavis for providing the number of datasets reanalyzed by the resources and list of phospho peptides. Thanks to Juan A. Vizcaino for the feedback and discussions about ProteomeXchange repositories.

Declaration of interest

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

Reviewer disclosures

Peer reviewers on this manuscript have no relevant financial or other relationships to disclose.

Geolocation information

Data sharing and reuse have become more common and standard for the proteomics community. This manuscript highlights major databases for storing proteomics data and the major challenges for data submission, dissemination, and reuse.

Data deposition

This manuscript does not contain any new data, no data was generated.

Additional information

Funding

This paper was not funded.