High-Recovery Pipette-Tip-Based Solid-Phase Extraction Using Polytetrafluoroethylene Disks Embedded with Chromatographic Particles

Pipette-tip-based solid-phase extraction (SPE) using PTFE fiber disks embedded with chromatographic particles has become a widely adopted method for peptide desalting in proteomics. Compared to conventional gravity-driven SPE cartridges, StageTip formats enable unidirectional, rapid loading and elution with minimal sample loss, allowing high recovery even from trace peptide amounts. Although such SPE disks are commercially available from multiple suppliers, their performance equivalence has not been systematically evaluated. The need for high-recovery desalting at low sample amounts has increased substantially as mass spectrometric sensitivity has advanced over the past two decades. To address this gap, we compared two structurally similar SDB-based SPE disks, supplied by company A and company B, and evaluated their peptide recovery performance using a StageTip-based workflow. When 20 ng of tryptic peptides derived from HeLa cells were loaded onto each disk type, substantial differences in recovery efficiency were observed. Company A yielded 3,957 unique peptides, whereas company B yielded 694, with 3,155 peptides commonly identified. Furthermore, the sum of peptide-ion intensities across the chromatographic time range was consistently higher for company A, indicating more efficient peptide retention and elution for both hydrophilic and hydrophobic peptides. These findings demonstrate that SDB-based SPE disks from different manufacturers, despite their similar appearance and construction, do not exhibit equivalent performance in low-input proteomics workflows.