A Solid-Phase Extraction Capture (SPEC) workflow in nanoliter volumes for fast, robust and ultrasensitive proteomics

Despite great progress, sample preparation remains an area for improvement in proteomics, particularly for low-input samples where conventional protocols lead to losses and incomplete digestion. We present Solid-Phase Extraction Capture (SPEC), a modular workflow that confines protein processing to nanoliter-scale volumes within C18 or ion-exchange tips. SPEC enables highly efficient proteolysis directly on the solid phase, minimizing surface losses and reagent dilution. A two-tip configuration further allows orthogonal phase combinations for optimal digestion and on-tip manipulation. Compared to alternative protocols, SPEC improves protein recovery while accelerating protein digestion which completes in minutes. The method is compatible with a diverse set of sample types and lysis conditions, including strong detergents, FFPE tissue, and muscle fibers. SPEC’s nanoliter digestion volume, high recovery, and flexible design make it a powerful tool for ultrasensitive and high-throughput proteomics, facilitating applications from spatial biology to clinical profiling. SPEC represents a universal proteome sample preparation protocol that spans all sample types, sensitivity levels, and throughput requirements.