Comprehensive and deep profiling of the plasma proteome with protein corona on zeolite NaY.

"dynamic light scattering (dls) zeta potential and confocal laser scanning microscopy (clsm) characterization are detailed in the supplementary data 2 3 this research was granted by the ethics committee of tianjin medical university cancer institute and hospital (ethical batch number: e2020610) and was conducted in strict adherence to the principles of the declaration of helsinki.; detailed sample preparation and digestion procedures for depleted plasma are shown in the supplementary data 2 6 2 6 1 dried peptide samples were resuspended in a loading buffer (3% acn 0 1% fa) with irt standards and analyzed on a thermo scientific ultimate 3000 uhplc system coupled with an orbitrap q exactive hf mass spectrometer.; the generation of the library for dia data analysis is detailed in the supplementary data 2 6 3 dried peptide samples were resuspended in a loading buffer (3% acn 0 1% fa) with irt standards and analyzed on a thermo scientific ultimate 3000 uhplc system coupled with an orbitrap q exactive hf mass spectrometer.; approximately 4000 proteins and 31000 peptides were identified from nay-ppc presenting a huge advantage compared to the 600 proteins and 4000 peptides that were obtained in the pure plasma control (see supplementary data 1 for a list of all identified proteins).; in direct data-independent acquisition (ddia) mode about 2500 proteins and 15000 peptides were identified in nay-ppc while only about 500 proteins and 3000 peptides were detected in pure plasma ( fig s2 ; supplementary data 1 ).; the results showed that the nay-ppc-based method identified more than 3100 proteins and 23000 peptides with 1 7- and 4 8-fold more proteins and 2 6- and 5 7-fold more peptides compared with the depleted plasma and pure plasma respectively ( figs3 d-f; supplementary data 1 ).; besides to save testing time the 10 replicates from different batches were tested using a 30 min effective gradient of dia ( supplementary data 2 ).; proteins adsorbed by nay were detected using the 60 min effective gradient and 120 min gradient in dda and dia modes with dda files processed with maxquant and dia processed with spectronaut ( supplementary data 3 ).; to further analyze the protein composition the relative protein abundance (rpa) of each protein in the three biological replicates of the nay-ppc group or plasma control group was first calculated which in turn led to the mean rpa of each protein in the nay-ppc group or plasma control group ( supplementary data 4 ).; as shown in fig 5 c the proportions of these proteins in the plasma control and the nay-ppc were compared respectively ( supplementary data 4 ).; then the proteins identified from the plasma control and nay-ppc were sorted by rpa from highest to lowest respectively and the cumulative rpa was calculated ( fig s3; supplementary data 4 ).; all of the above data indicate that our approach based on nay-ppc can remove high-abundance proteins to some extent thus enhancing the detection of low-abundance proteins3 5 to determine the dynamic range as well as the detection depth covered by our method the identified proteins were mapped against the human plasma peptideatlas [ ] ( fig 6 ; supplementary data 5 ).; in total 4804 proteins were identified in 45 discovery cohorts and 3415 were present in more than 70% of the samples ( fig 7 a; supplementary data 6 ).; there were 470 proteins differentially expressed in the tumor group compared to the health group ( p -adjust <0 05 fc (t/h) > 2 or <0 5) including 283 proteins upregulated and 187 downregulated in tumors ( fig 7 b; supplementary data 6 )."

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

"This work was supported by the National Natural Science Foundation of China (Grant No: 51773151). Congcong Ma: Methodology, Validation, Formal analysis, Investigation, Writing - Original draft preparation, Reviewing and Editing, Visualization; Yanwei Li: Resources, Project administration; Jie Li: Resources, Writing - Original draft preparation, Supervision; Lei Song: Software, Data curation, Visualization, Project administration; Liangyu Chen: Software, Data curation, Visualization, Project administration; Na Zhao: Validation, Formal analysis, Visualization, Writing - Reviewing and Editing; Xueping Li: Validation, Formal analysis; Ning Chen: Validation, Supervision; Lixia Long: Validation, Resources; Jin Zhao: Conceptualization, Validation, Investigation, Supervision, Funding acquisition, Writing - Reviewing and Editing; Xin Hou: Validation, Investigation, Supervision, Funding acquisition, Writing - Reviewing and Editing; Li Ren: Conceptualization, Resources, Supervision; Xubo Yuan: Conceptualization, Investigation, Resources, Project administration, Funding acquisition, Writing - Reviewing and Editing."