Figure 4.

Strategy for PDX MS data quantitation. A. The workflow of SPA strategy. MS data of PDX samples were searched against HM database and peptides were sorted into three categories according to sequence uniqueness. SH peptides were allocated according to the ratio of summed HU peptide intensity to summed MU peptide intensity. HU peptides, combined with human proportion from SH peptides, were used for protein assembling and quantitation. B. Quantitation of mixing ratios of human proteins to mouse proteins for the proteome benchmark dataset via SPA. Ratios of summed HU peptide intensity to MU peptide intensity, ratios of summed HU and SH peptide intensity to MU peptide intensity, and the overall human-to-mouse ratios by SPA for four standard sets were calculated, respectively. The percentages of the identified proteins assigned to HU, MU, and SH were colored into orange, blue, and gray, respectively.