Additional file 2 of A semi-tryptic peptide centric metaproteomic mining approach and its potential utility in capturing signatures of gut microbial proteolysis

Additional file 1: Table S1. Microbial semi-tryptic peptides and the cleavage sites in the fecal metaproteomes. Table S2 Human semi-tryptic peptides and the cleavage sites in the fecal metaproteomes. Table S3 Microbial semi-tryptic peptides and the cleavage sites in the ascending colon (AsC) MLI metaproteomes. Table S4 Microbial semi-tryptic peptides and the cleavage sites in the descending colon (DeC) MLI metaproteomes. Table S5. Microbial semi-tryptic peptides and the cleavage sites in the terminal ileum (TI) MLI metaproteomes. Table S6. Human semi-tryptic peptides and the cleavage sites in the ascending colon (AsC) MLI metaproteomes. Table S7. Human semi-tryptic peptides and the cleavage sites in the descending colon (DeC) MLI metaproteomes. Table S8. Human semi-tryptic peptides and the cleavage sites in the terminal ileum (TI) MLI metaproteomes. Table S9-S10. Human full tryptic peptides in fecal metaproteomes. Table S11. Microbial full tryptic peptides in the ascending colon (AC) MLI metaproteomes. Table S12. Human full tryptic peptides in the ascending colon (AsC) MLI metaproteomes. Table S13. Microbial full tryptic peptides in the descending colon (DeC) MLI metaproteomes. Table S14. Human full tryptic peptides in the descending colon (DeC) MLI metaproteomes. Table 15. Microbial full tryptic peptides in the terminal ileum (TI) MLI metaproteomes. Table 16. Human full tryptic peptides in the terminal ileum (TI) MLI metaproteomes. Table S17. NRASP of 20 major taxonomic sub-groups identified in fecal metaproteomes. Table S18. NRASP of 35 major biological processes identified in fecal metaproteomes. Table S19. NRASP of 32 major enzyme subclasses identified in fecal metaproteomes. Table S20. Peptides and altered NRASP. Table S21. Peptides identified in the Escherichia coli proteome using reference database and one-step database searching. Table S22. NRASP of biological processes identified in Escherichia coli proteome. Table S23. Relative abundance of 81 major taxonomic sub-groups identified in fecal metaproteomes. Table S24. NRASP of 156 major biological processes identified in fecal metaproteomes. Table S25. NRASP of 195 major enzyme sub-subclasses identified in fecal metaproteomes. Table S26. Alterations of amino acid frequencies around the cleavage sites in the fecal microbial proteins. Table S27. Alterations of amino acid frequencies around the cleavage sites in the fecal human proteins. Table S28. NRASP of 57 major biological processes identified in AsC metaproteomes. Table S29. NRASP of 56 major biological processes identified in DeC metaproteomes. Table S30. NRASP of 51 major biological processes identified in TI metaproteomes. Table S31. Alterations of amino acid frequencies around the cleavage sites in the ascending colon (AsC) MLI microbial proteins. Table S32. Alterations of amino acid frequencies around the cleavage sites in the decending colon (DeC) MLI microbial proteins. Table S33. Alterations of amino acid frequencies around the cleavage sites in the terminal ileum (TI) MLI microbial proteins. Table S34. Alterations of amino acid frequencies around the cleavage sites in the ascending colon (AsC) MLI human proteins. Table S35. Alterations of amino acid frequencies around the cleavage sites in the decending colon (DeC) MLI human proteins. Table S36 Alterations of amino acid frequencies around the cleavage sites in the terminal ileum (TI) MLI human proteins. Table S36 Alterations of amino acid frequencies around the cleavage sites in the terminal ileum (TI) MLI human proteins. Fig. S1. Altered fecal metaproteomes of IBD at different levels revealed by full tryptic peptide based normalized relative abundance. Representative alterations are illustated at different taxonomic levels (a) as well as in different biological processes (b) and enzyme sub-classes (c). Dunn-Bonferroni post-hoc analysis following Kruskal-Wallis test was employed to detect significant difference among three groups (CD, Ctrl, and UC). *P < 0.05 versus Ctrl; **P < 0.01 versus Ctrl; ***P < 0.001 versus Ctrl; # P < 0.05 (CD versus UC); ##P < 0.01 (CD versus UC); ### P < 0.001 (CD versus UC). Fig. S2. Principal coordinates analysis (PCoA) based on Bray–Curtis index of semi-tryptic peptide intensity in the fecal metaproteomes. Fig. S3. Altered amino acid frequencies around the cleavage sites of human proteins in fecal metaproteomes of IBD. Fig. S4. Microbial proteins and human proteins in fecal samples can exhibit similar or reversed alteration trends in certain positions around the cleavage site in IBD. Dunn-Bonferroni post-hoc analysis following Kruskal-Wallis test was employed to detect significant group difference. *P < 0.05 versus Ctrl; **P < 0.01 versus Ctrl; ***P < 0.001 versus Ctrl. Fig. S5 Hierarchical clustering analysis of altered amino acid frequencies around the cleavage sites of human proteins in MLI metaproteome of IBD. a ascending colon, b descending colon, c terminal ileum. Fig. S6. Microbial proteins and human proteins in MLI samples can exhibit similar or reversed alteration trends in certain positions around the cleavage site in IBD. a ascending colon, b descending colon, c terminal ileum. Dunn-Bonferroni post-hoc analysis following Kruskal-Wallis test was employed to detect significant group difference. *P < 0.05 versus Ctrl; **P < 0.01 versus Ctrl; ***P < 0.001 versus Ctrl. Fig S7. Increased human protease inhibitors (a) and immunoglobulins (b) in IBD revealed by the label-free quantification (LFQ) intensity