From proteome definition to modern proteomics: Mass spectrometry and emerging affinity-based platforms including SomaScan, Olink PEA, and Nautilus voyager™.

Abstract

Proteomics has evolved from a predominantly mass spectrometry (MS)-based discipline into a broader analytical field that includes complementary affinity-based technologies for large-scale protein characterization. MS remains the cornerstone of modern proteomics because it enables unbiased identification and quantification of proteins, post-translational modifications, and proteoforms. The need for high-throughput, low-input, and scalable protein profiling has nevertheless accelerated the adoption of SomaScan, Olink Proximity Extension Assay (PEA), and emerging single-molecule platforms such as Nautilus Voyager™. Although all use affinity recognition, they interrogate different molecular features aptamer-binding surfaces, paired antibody epitopes, or cumulative binding patterns used to infer intact-protein identity and should therefore be viewed as complementary rather than interchangeable. This review summarizes the evolution, principles, workflows, strengths, limitations, and representative applications of MS, SomaScan, Olink PEA, and Nautilus Voyager, and discusses their integration in biomarker discovery, population proteomics, and precision medicine. Emerging opportunities in artificial intelligence, single-cell and spatial proteomics, multi-omics integration, and next-generation affinity reagents are also considered.