Post-Column Dead Volume as a Critical Determinant in Low-Input, High-Throughput Proteomics

Abstract Post-column dead volume resulting from union-separated emitters and other sources can be a major contributor to extra-column band broadening in nano-flow liquid chromatography, yet its impact across practical configurations has not been studied systematically. Here, we evaluate the impact of post-column dead volume (PCDV) on chromatographic performance and proteome depth by comparing integrated and non-integrated column configurations connected through unions or valves across a broad range of column inner diameters, flow rates and gradient lengths. We show that PCDV effects significantly increase peak widths, particularly for short gradients and low flow rates. Increased PCDV also results in dramatically reduced proteome coverage, particularly for low-input samples. Surprisingly, eliminating PCDV through integrated emitters increased quantitative precision under virtually all tested conditions despite the narrower peaks leading to fewer data points per peak. When using a high-throughput LC platform operated at 288 samples per day (5 min sample-to-sample time), up to 35.8% improvement in proteome coverage was achieved for single-cell proteomics for an integrated emitter relative to a union-connected emitter. These findings underscore the importance of minimizing post-column dead volume for high-sensitivity and high-throughput nanoLC-MS analyses.