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

附加文件1：表S1。粪便宏蛋白质组中的微生物半胰蛋白酶肽及其切割位点。
表S2 粪便宏蛋白质组中的人类半胰蛋白酶肽及其切割位点。
表S3 升结肠（AsC）MLI宏蛋白质组中的微生物半胰蛋白酶肽及其切割位点。
表S4 降结肠（DeC）MLI宏蛋白质组中的微生物半胰蛋白酶肽及其切割位点。
表S5 回肠末端（TI）MLI宏蛋白质组中的微生物半胰蛋白酶肽及其切割位点。
表S6 升结肠（AsC）MLI宏蛋白质组中的人类半胰蛋白酶肽及其切割位点。
表S7 降结肠（DeC）MLI宏蛋白质组中的人类半胰蛋白酶肽及其切割位点。
表S8 回肠末端（TI）MLI宏蛋白质组中的人类半胰蛋白酶肽及其切割位点。
表S9~S10 粪便宏蛋白质组中的人类全胰蛋白酶肽。
表S11 升结肠（AC）MLI宏蛋白质组中的微生物全胰蛋白酶肽。
表S12 升结肠（AsC）MLI宏蛋白质组中的人类全胰蛋白酶肽。
表S13 降结肠（DeC）MLI宏蛋白质组中的微生物全胰蛋白酶肽。
表S14 降结肠（DeC）MLI宏蛋白质组中的人类全胰蛋白酶肽。
表15 回肠末端（TI）MLI宏蛋白质组中的微生物全胰蛋白酶肽。
表16 回肠末端（TI）MLI宏蛋白质组中的人类全胰蛋白酶肽。
表S17 粪便宏蛋白质组中鉴定出的20个主要分类学亚组的标准化相对特异肽丰度（NRASP）。
表S18 粪便宏蛋白质组中鉴定出的35个主要生物学过程的标准化相对特异肽丰度（NRASP）。
表S19 粪便宏蛋白质组中鉴定出的32个主要酶亚类的标准化相对特异肽丰度（NRASP）。
表S20 肽段与变化的标准化相对特异肽丰度。
表S21 采用参考数据库与单步数据库搜索在大肠杆菌蛋白质组中鉴定出的肽段。
表S22 大肠杆菌蛋白质组中鉴定出的生物学过程的标准化相对特异肽丰度（NRASP）。
表S23 粪便宏蛋白质组中鉴定出的81个主要分类学亚组的相对丰度。
表S24 粪便宏蛋白质组中鉴定出的156个主要生物学过程的标准化相对特异肽丰度（NRASP）。
表S25 粪便宏蛋白质组中鉴定出的195个主要酶亚亚类的标准化相对特异肽丰度（NRASP）。
表S26 粪便微生物蛋白质切割位点周围氨基酸频率的变化。
表S27 粪便人类蛋白质切割位点周围氨基酸频率的变化。
表S28 升结肠（AsC）宏蛋白质组中鉴定出的57个主要生物学过程的标准化相对特异肽丰度（NRASP）。
表S29 降结肠（DeC）宏蛋白质组中鉴定出的56个主要生物学过程的标准化相对特异肽丰度（NRASP）。
表S30 回肠末端（TI）宏蛋白质组中鉴定出的51个主要生物学过程的标准化相对特异肽丰度（NRASP）。
表S31 升结肠（AsC）MLI微生物蛋白质切割位点周围氨基酸频率的变化。
表S32 降结肠（DeC）MLI微生物蛋白质切割位点周围氨基酸频率的变化。
表S33 回肠末端（TI）MLI微生物蛋白质切割位点周围氨基酸频率的变化。
表S34 升结肠（AsC）MLI人类蛋白质切割位点周围氨基酸频率的变化。
表S35 降结肠（DeC）MLI人类蛋白质切割位点周围氨基酸频率的变化。
表S36 回肠末端（TI）MLI人类蛋白质切割位点周围氨基酸频率的变化。
表S36 回肠末端（TI）MLI人类蛋白质切割位点周围氨基酸频率的变化。
图S1：基于全胰蛋白酶肽标准化相对丰度揭示的炎症性肠病（IBD）不同层面的粪便宏蛋白质组变化。在不同分类学层面（a）以及不同生物学过程（b）和酶亚类（c）中展示了典型变化。采用克鲁斯卡尔-沃利斯检验后进行Dunn-Bonferroni事后检验，以检测三组（克罗恩病（CD）、对照组（Ctrl）、溃疡性结肠炎（UC））之间的显著差异。*P < 0.05 与对照组相比；**P < 0.01 与对照组相比；***P < 0.001 与对照组相比；# P < 0.05（CD与UC相比）；## P < 0.01（CD与UC相比）；### P < 0.001（CD与UC相比）。
图S2：基于粪便宏蛋白质组中半胰蛋白酶肽强度的布雷-柯蒂斯指数的主坐标分析（PCoA）。
图S3：IBD患者粪便宏蛋白质组中人类蛋白质切割位点周围氨基酸频率的变化。
图S4：IBD患者粪便样本中的微生物蛋白质与人类蛋白质在切割位点周围的某些位置可呈现相似或相反的变化趋势。采用克鲁斯卡尔-沃利斯检验后进行Dunn-Bonferroni事后检验，以检测组间显著差异。*P < 0.05 与对照组相比；**P < 0.01 与对照组相比；***P < 0.001 与对照组相比。
图S5：IBD患者MLI宏蛋白质组中人类蛋白质切割位点周围氨基酸频率变化的层级聚类分析。a 升结肠，b 降结肠，c 回肠末端。
图S6：IBD患者MLI样本中的微生物蛋白质与人类蛋白质在切割位点周围的某些位置可呈现相似或相反的变化趋势。a 升结肠，b 降结肠，c 回肠末端。采用克鲁斯卡尔-沃利斯检验后进行Dunn-Bonferroni事后检验，以检测组间显著差异。*P < 0.05 与对照组相比；**P < 0.01 与对照组相比；***P < 0.001 与对照组相比。
图S7：通过无标记定量（LFQ）强度揭示的IBD患者体内升高的人类蛋白酶抑制剂（a）与免疫球蛋白（b）。