The privilege of a new core facility: Optimising technical repeatability and workflow efficiency in proteomics across diverse biological matrices

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Bottom-up proteomics relies on efficient and repeatable sample preparation for accurate protein identification and precise quantification. This study evaluates the performance of adapted SPEED (Sample Preparation by Easy Extraction and Digestion) protocols, a simplified, detergent-free approach tailored for various biological matrices, including lysis-resistant samples. Protein extraction and denaturation steps were refined for 12 biological matrices enabling standardized, high-throughput, and scalable proteomics analysis on 96-well plates. For tissue samples requiring downstream applications like Western blotting, we used a low-detergent RIPA buffer, ensuring robust protein extraction and epitope integrity. Notably, the protocols demonstrate remarkable down-scalability, enabling robust proteomics measurements from as few as 3,000 cells per sample and even down to 300 cells per injection. Key advancements include a 30-minute nLC-MS/MS run, significantly enhancing throughput, and leveraging the power of DIA-PASEF using thoroughly optimized DIA-windows to enhance proteome coverage. These adaptations streamline workflows, enabling proteomics analyses in matrices with challenging physical and biochemical properties. This study underscores the importance of early-stage optimization and feasibility testing in proteomics pipelines to inform study design and sample selection. By showcasing robust, scalable adaptations of the SPEED protocol, we provide a foundation for reproducible, high-throughput proteomic studies across diverse biological contexts.

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