With the development of mass spectrometry(MS)-based proteomics technologies,patient-derived xenograft(PDX),which is generated from the primary tumor of a patient,is widely used for the proteome-wide analysis of cancer...With the development of mass spectrometry(MS)-based proteomics technologies,patient-derived xenograft(PDX),which is generated from the primary tumor of a patient,is widely used for the proteome-wide analysis of cancer mechanism and biomarker identification of a drug.However,the proteomics data interpretation is still challenging due to complex data deconvolution from the PDX sample that is a cross-species mixture of human cancerous tissues and immunodeficient mouse tissues.In this study,by using the lab-assembled mixture of human and mouse cells with different mixing ratios as a benchmark,we developed and evaluated a new method,SPA(shared peptide allocation),for protein quantitation by considering the unique and shared peptides of both species.The results showed that SPA could provide more convenient and accurate protein quantitation in human–mouse mixed samples.Further validation on a pair of gastric PDX samples(one bearing FGFR2 amplification while the other one not)showed that our new method not only significantly improved the overall protein identification,but also detected the differential phosphorylation of FGFR2 and its downstream mediators(such as RAS and ERK)exclusively.The tool pdx SPA is freely available at https://github.com/LiLab-Proteomics/pdx SPA.展开更多
基金supported by the Special Project on Precision Medicine under the National Key R&D Program of China(Grant No.2017YFC09066600)the National Natural Science Foundation of China(Grant Nos.31871329,31670066,and 31271416)+1 种基金the National Science&Technology Major Project“Key New Drug Creation and Manufacturing Program”,China(Grant No.2018ZX09711002007)the Natural Science Foundation of Shanghai,China(Grant No.17ZR1413900)。
文摘With the development of mass spectrometry(MS)-based proteomics technologies,patient-derived xenograft(PDX),which is generated from the primary tumor of a patient,is widely used for the proteome-wide analysis of cancer mechanism and biomarker identification of a drug.However,the proteomics data interpretation is still challenging due to complex data deconvolution from the PDX sample that is a cross-species mixture of human cancerous tissues and immunodeficient mouse tissues.In this study,by using the lab-assembled mixture of human and mouse cells with different mixing ratios as a benchmark,we developed and evaluated a new method,SPA(shared peptide allocation),for protein quantitation by considering the unique and shared peptides of both species.The results showed that SPA could provide more convenient and accurate protein quantitation in human–mouse mixed samples.Further validation on a pair of gastric PDX samples(one bearing FGFR2 amplification while the other one not)showed that our new method not only significantly improved the overall protein identification,but also detected the differential phosphorylation of FGFR2 and its downstream mediators(such as RAS and ERK)exclusively.The tool pdx SPA is freely available at https://github.com/LiLab-Proteomics/pdx SPA.
