3D-Printed Device for Consistent and High-Throughput Peptide Sample Clean-up Using StageTips

Mass spectrometry (MS) is a fundamental technology for the study of proteomics. A core technique for MS analysis is solid-phase extraction (SPE) for the removal of contaminants and sample concentration, and StageTips are one of the most commonly used devices used for SPE in modern proteomics workflows. Here, we detail a device that can accommodate up to 96 StageTips enabling high-speed centrifugal-based processing of StageTips, including collection into PCR tubes, or 96-well plates, simplifying the processing of samples for MS analysis. The device can be rapidly and economically manufactured using a 3D printer employing fused deposition modelling. We show that high impact polystyrene (HIPS) is a particularly suitable material for building this device, providing good chemical resistance and is able to withstand high centrifugal speeds to enable repeated use. We provide detailed schematics as well as the corresponding CAD files for the community, enabling reproduction of the device on any common 3D printer model. Using an optimized protocol, we show that our tip spinner device provides similar peptide identifications and comparable inter-sample consistency than previously established centrifugation-based cleanup on individual StageTips. As such, this apparatus facilitates greater throughput in sample preparation for mass spectrometry, without detracting from sample quality.