A Suspension-Trapping Protocol for Bottom-Up Proteomics Sample Preparation

Bottom-up proteomics workflows encompass several key stages, including sample preparation, data acquisition, and data analysis. Of these, sample preparation is the initial and critical stage, as it significantly influences the depth, reproducibility, and reliability of subsequent mass spectrometry-based analyses. While several main digestion strategies exist, including in-gel, in-solution, and filter-aided methods, each presents distinct trade-offs in terms of throughput, contamination removal, and applicability to complex biological matrices. The Suspension Trapping (S-Trap) method offers a compelling alternative by efficiently capturing and digesting proteins while removing interferents like sodium dodecyl sulfate (SDS), which can compromise downstream LC-MS/MS performance. This protocol details a S-Trap workflow optimized for biofluid proteomics, specifically plasma, serum, and cerebrospinal fluid (CSF). We describe two complementary formats: a manual tube-based procedure for individual or small-batch samples and a 96-well-plate-based system enabling high-throughput processing. The protocol integrates optional high-abundance protein depletion to enhance coverage of low-abundance analytes and includes steps for reduction, alkylation, digestion, and peptide elution for low total protein content samples, such as plasma, serum, and cerebrospinal fluid. By providing a detailed protocol, this work aims to improve the consistency and accessibility of S-Trap-based sample preparation, facilitating robust and reproducible discoveries in bottom-up proteomics. Key features • Plasma/serum/cerebrospinal fluid sample preparation for bottom-up proteomics. • Lab Suspension Trapping (S-Trap)-based digestion for efficient detergent removal and high peptide recovery. • Optimized for challenging samples (e.g., CSF, plasma) with low protein concentration or high lipid content. • Includes both single-tube and high-throughput 96-well plate formats for flexible experimental design.