Fig. 4

a Workflow for proteomic data analysis: (b) Graphical representation of all the normalised data obtained through Trans proteomics pipeline (TPP) tools. We have used three search engines commonly using the Uniprot Cricetulus griseus (Hamster), Mus musculus (Mouse) and Rattus norvegicus (Rat) database (Comet, Tandem, Mascot). Note: Control- Normal CHO-K1 cells, MSN- Mesoporous silica nanoparticle, ZnO- Zinc oxide nanoparticle, MWCNT- Multi-Walled Carbon Nanotube, Nanoparticle.114–117 are iTRAQ isobaric labels. b Functional classification differentially abundant proteins after MSN15, MWCNT5, and ZnO5 NPs treatment to CHO-K1 Cells: The pathways or bio-effects related to MSN15, MWCNT5, and ZnO5 NPs were determined by KEGG based annotation. The percentages of the differential proteins involved in the bio-effects of NPs were shown in the pie chart. 21% membrane trafficking, 18% chromosome, and associated protein, and 9% ubiquitin system classified to originate from genetic information. Signaling and cellular processes were identified 29% related to exosomal proteins, 13% cytoskeleton and transporter proteins. Metabolic associated proteins 30% assigned to the peptidases, 27% to the protein kinase, and 22% to the protein phosphatase of the total proteome. c Nanoparticles induces changes in the CHO-K1 Cell Proteome: In total, 6244 proteins were identified in NPs-treated and control CHO-K1 cells (peptide FDR p-value < 0.05). On fixed fold change cutoff at >|1.5|, total 1188 (19%) proteins were differentially expressed by the treatment of MSN15 (1070 upregulated and 118 down-regulated), 1181 (18.91%) proteins to MWCNT5 (1105 upregulated and 76 down-regulated) and 1100 (17.61%) proteins to ZnO5 NPs (835 upregulated and 265 down-regulated). Overlap among proteins up and down-regulated by MSN15, MWCNT5, and ZnO5 NPs. d Volcano plot elucidates significantly differentially abundant proteins in the CHO-K1 cell line after NPs treatment: The volcano plot displaying the fold changes (x-axis) vs the − log₁₀ p-values (y-axis) for individual protein. An essential feature in the volcano plot selected by the t-statistics. The proteins are highlighted in each panel shows with larger and smaller fold changes (red). The upregulated proteins represented in the right side of the plot and the downregulated proteins represented in the left side of the plot. Note the values are on a log scale so that differential expression values can be plotted symmetrically. e Gene Ontology analysis: Gene Ontology (GO) analysis was performed of differentially regulated proteins by the MSN15, MWCNT5, and ZnO5 NPs. The bar graph indicate the upregulated and downregulated GO enrichment for the cellular component, pathway, molecular function and biological function of the proteins. The orange bars shows proteins enriched by MSN15 NPs, green bars show proteins enriched by MWCNT5, and sky blue bars show proteins enriched by ZnO5 NPs. The value of FDR < 0.05 was considered statistically significant