From Identification to Integration: Twenty-Five Years of Proteomics and Metabolomics through the Pages of the Journal of Proteome Research

As the American Chemical Society marks its 150th anniversary, it is a fitting moment to reflect on how a young analytical discipline, proteomics, matured into a central pillar of the chemical and biological sciences and how the Journal of Proteome Research (JPR) chronicled and guided that transformation. Founded at the dawn of shotgun proteomics, JPR has published pivotal advances in separation, ionization, computational interpretation, quantitative strategies, and biological applications. In this Perspective, we trace that arc from the first near-complete eukaryotic proteomes through the quantitative and post-translational era, the computational turn, and the current high-throughput, integrative, and artificial-intelligence-assisted phase. Along the way, we highlight how the same infrastructure enabled mass spectrometry-based metabolomics, yielding an integrated framework for molecular phenotyping.