Quantification strategy for PDX MS data

Data interpreting of PDX proteome is still a problem because with the growth of human cancerous tissue in an immunodeficient mouse, the endothelial cells and fibroblasts from the host mouse replaced human stromal components, making PDX sample a mixture of human and mouse cells. In this study, we created four human and mouse protein mixtures with different human protein percentages as the standard testing sets. We established an easy algorithm to fit the known proportions and used this strategy on a pair of PDX samples. Our data suggested that our new algorithm is feasible and may help to offer more information on PDX proteome data analysis.