A highly efficient protein corona-based proteomic analysis strategy for the discovery of pharmacodynamic biomarkers.

"the dda data processing of lc-ms/ms and bioinformatic analyses are detailed in the supplementary data 2 8 each experiment was repeated at least thrice and presented as mean ?; a total of 1070 proteins were detected in the nano group while only 573 proteins were detected in the serum group (supplementary data 1).; however our results indicated that si-ionps could simultaneously enrich the low-abundance proteins and deplete high-abundance proteins from the serum samples ( table s3 and supplementary data 1).; after pc-based proteomic analysis986 1078 and 965 proteins were quantified in control cia and mtx groups ( n = 3) respectively (supplementary data 2).; as shown in figs6 b and c 485 deps were detected in the cia/control comparison (399 up-regulated and 86 down-regulated) while 519 deps were detected in the cia/mtx comparison (409 up-regulated and 110 down-regulated) suggesting that pc can be potentially used for in-depth discovery of pharmacodynamic biomarkers and drug targets (supplementary data 3).; the specific information of bps in the go term is provided in supplementary data 4.; appendix a supplementary data the following are the supplementary data to this article: supplementary data_manuscript number jpa-d-22-00121r3 docx supplementary data_manuscript number jpa-d-22-00121r3 docx supplementary data 1 xlsx supplementary data 1 xlsx supplementary data 2 xlsx supplementary data 2 xlsx supplementary data 3 xlsx supplementary data 3 xlsx supplementary data 4 xlsx supplementary data 4 xlsx acknowledgments we gratefully acknowledge financial support from the (grant nos: 2020yfa0908000 and 2020yfe0205100) the innovation team and talents cultivation program of national administration of traditional chinese medicine (grant no: zyycxtd-c-202002) the (grant nos: 82074098 82173914 and 82141001) the innovation fund (grant nos: ci2021a05101 and ci2021a05104) the fundamental research funds for the central public welfare research institutes (grant nos: zz15-yq-065 zz14-yq-058 zz14-yq-050 zz14-yq-051 zz14-yq-052 zz14-nd-010 zz15-nd-10 and zz14-fl-002) and the (grant no: yjkyyq20210025)."

"Declaration of competing interest The authors declare that there are no conflicts of interest."

"We gratefully acknowledge financial support from the 10.13039/501100012166National Key Research and Development Program of China (Grant Nos.: 2020YFA0908000 and 2020YFE0205100), the Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine (Grant No.: ZYYCXTD-C-202002), the 10.13039/501100001809National Natural Science Foundation of China (Grant Nos.: 82074098, 82173914, and 82141001), the 10.13039/501100005892CACMS Innovation Fund (Grant Nos.: CI2021A05101 and CI2021A05104), the Fundamental Research Funds for the Central Public Welfare Research Institutes (Grant Nos.: ZZ15-YQ-065, ZZ14-YQ-058, ZZ14-YQ-050, ZZ14-YQ-051, ZZ14-YQ-052, ZZ14-ND-010, ZZ15-ND-10, and ZZ14-FL-002), and the 10.13039/501100002367Chinese Academy of Sciences (Grant No.: YJKYYQ20210025)."