SWIFT-GP: A Rapid and Automated Platform for the Sensitive Profiling of Site-Specific Glycans from Trace Samples

Sensitive glycoproteomic profiling of limited clinical samples is often hindered by labor-intensive, multistep sample preparation and the substantial sample loss inherent to manual workflows. In this study, we developed SWIFT-GP (Seamless Workflow for Intact Fast Trace-level GlycoProteomics), an integrated platform that combines an optimized rapid digestion protocol with an online three-column enrichment and separation system and a match-between-runs (MBR) strategy for the fast and sensitive profiling of intact glycopeptides. By utilizing an integrated valve-switching configuration that minimizes manual handling, the total time from live cells to collected glycopeptide MS spectra was reduced from over 27 to 3 h. Further integration with the MBR strategy markedly expanded the identification of IGPs while effectively reducing the missing values inherent in low-input sample analysis. The performance of SWIFT-GP was demonstrated by processing trace serum samples and microscale cellular inputs. Using 1 μg serum protein as the starting material, followed by rapid digestion and online enrichment, 986 intact glycopeptides (IGPs) were reproducibly quantified. Notably, over 1,700 IGPs can be recovered from 104 cancer cells. Overall, SWIFT-GP provides an efficient and sensitive solution for site-specific glycosylation profiling of restricted clinical specimens, supporting applications in high-throughput and trace-level glycoproteomic research.