Protocol for N-glycoproteomic enrichment of cancer cell-surface proteins in patient-derived xenografts

Cell surface proteins are valuable drug targets and biomarkers, yet are often obscured in traditional mass spectrometry-based proteomics datasets. Leveraging the high prevalence of N-glycosylation on extracellular proteins, we present a protocol for N-glycoproteomic profiling of patient-derived xenografts to enable in vivo characterization of cancer cell-derived surface proteomes. We describe steps for lysis, chemical enrichment, enzymatic modification, and tumor-stroma deconvolution analysis. We also provide a scalable strategy to improve the detection and prioritization of surface proteins in cancers. For complete details on the use and execution of this protocol, please refer to Govindarajan et al.¹.