Mouse Stromal Cells Confound Proteomic Characterization and Quantification of Xenograft Models.

ABSTRACT: Xenografts are essential models for studying cancer biology and developing oncology drugs, and are more informative with omics data. Most reported xenograft proteomics projects directly profiled tumors comprising human cancer cells and mouse stromal cells, followed by computational algorithms for assigning peptides to human and mouse proteins. We evaluated the performance of three main algorithms by carrying out benchmark studies on a series of human and mouse cell line mixtures and a set of liver patient-derived xenograft (PDX) models. Our study showed that approximately half of the characterized peptides are common between human and mouse proteins, and their allocations to human or mouse proteins cannot be satisfactorily achieved by any algorithm. As a result, many human proteins are err

SUBMITTER: Shi Z 

PROVIDER: S-EPMC10035517 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature