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Nanobore reversed-phase HPLC has become a mainstay for protein identification by modern tandem mass spectrometry. Enhanced robustness and versatility is obtained with trapping columns for on-line preconcentration and desalting of samples. Trapping columns of varying sizes and packing materials are available, yet few configurations are available for 75-μm i.d. packed-tip columns frequently employed in high-sensitivity work. Using a novel fluoropolymer and PEEK-based zero-dead-volume fitting with packed-tip, silica-fritted capillary columns, variable trap column geometries, and column chemistry combinations were investigated toward optimizing chromatographic performance in a typical nanobore RP-HPLC-MS system.