Progress and trends on machine learning in proteomics during 1997-2024: a bibliometric analysis

Despite growing interest in the application of machine learning (ML) in proteomics, a comprehensive and systematic mapping of this research domain has been lacking. This study addresses this gap by conducting the first large-scale bibliometric analysis focused exclusively on ML-driven proteomics, aiming to elucidate its knowledge structure, development trajectory, and emerging research trends.

A total of 5,156 publications from the Web of Science Core Collection (1997-2024) were retrieved and analyzed. Bibliometric tools including CiteSpace 6.4.R1, VOSviewer 1.6.18, Scimago Graphica, and the R package bibliometrix were used to extract and visualize key bibliometric indicators. After data cleaning and de-duplication, analyses were conducted on keyword co-occurrence, citation networks, leading journals, influential authors, and institutional collaboration patterns to construct a comprehensive landscape of ML applications in proteomics.

The number of publications has grown exponentially since 2010, with an average annual growth rate of 12.53% and a notable surge of 65.14% occurring between 2019 and 2020. The United States emerged as the most productive country, while the Chinese Academy of Sciences led among institutions. AlphaFold2-related research received the highest citations, reflecting the transformative role of deep learning in protein structure prediction. Thematic clustering revealed key research foci, including deep learning algorithms, protein-protein interaction prediction, and integrative multi-omics analysis. The field is characterized by strong interdisciplinary convergence, involving computer science, molecular biology, and clinical research. High-impact journals and influential authors were also identified, providing benchmarks for academic influence and collaboration.

This study offers the first comprehensive bibliometric analysis of ML in proteomics, revealing key themes such as deep learning, pretrained models, and multi-omics integration. Future efforts should focus on building interpretable models, enhancing cross-disciplinary collaboration, and ensuring secure, standardized data use to advance precision medicine.

https://doi.org/10.17605/OSF.IO/F4WUG.