Aptamer-based multiplexed proteomic technology for biomarker discovery was developed to enable the simultaneous measurement of thousands of proteins from small sample volumes. This technology uses chemically modified nucleotides to enhance the physicochemical diversity of aptamers, which are selected through a process called SELEX. The resulting aptamers, known as SOMAmers, have high affinity and specificity for proteins and are used in a multiplexed proteomics assay that transforms protein concentration signatures into DNA aptamer concentration signatures, quantified on a DNA microarray. The assay allows for the identification of biomarkers in clinical samples, such as those from patients with chronic kidney disease (CKD). The technology demonstrated the ability to identify two well-known CKD biomarkers and 58 additional potential biomarkers. The assay has a low limit of detection (1 pM median), a dynamic range of 7 logs (100 fM–1 μM), and a median coefficient of variation of 5%. The technology is highly reproducible and scalable, enabling the discovery of novel biomarkers for various disease states. The study highlights the potential of this technology to advance evidence-based medicine by providing unbiased, high-throughput biomarker discovery.Aptamer-based multiplexed proteomic technology for biomarker discovery was developed to enable the simultaneous measurement of thousands of proteins from small sample volumes. This technology uses chemically modified nucleotides to enhance the physicochemical diversity of aptamers, which are selected through a process called SELEX. The resulting aptamers, known as SOMAmers, have high affinity and specificity for proteins and are used in a multiplexed proteomics assay that transforms protein concentration signatures into DNA aptamer concentration signatures, quantified on a DNA microarray. The assay allows for the identification of biomarkers in clinical samples, such as those from patients with chronic kidney disease (CKD). The technology demonstrated the ability to identify two well-known CKD biomarkers and 58 additional potential biomarkers. The assay has a low limit of detection (1 pM median), a dynamic range of 7 logs (100 fM–1 μM), and a median coefficient of variation of 5%. The technology is highly reproducible and scalable, enabling the discovery of novel biomarkers for various disease states. The study highlights the potential of this technology to advance evidence-based medicine by providing unbiased, high-throughput biomarker discovery.