Protocol for constructing in vivo and in vitro models integrating clinical and proteomic subtypes of chordoma

Here, we present a protocol for constructing both in vivo and in vitro models of chordoma, integrating clinical and proteomic subtyping to enable a comprehensive analysis. We detail the steps for tissue sample preparation and tandem mass tag proteomic analysis and apply non-negative matrix factorization for molecular classification. Furthermore, we classify chordoma cell lines and establish cell-derived xenograft (CDX) and patient-derived xenograft (PDX) models in mice for investigating drug response. For complete details on the use and execution of this protocol, please refer to Yin et al.¹.