PTMoreR: a motif-centric analysis enabling cross-species PTM mapping and comparative phosphoproteomics across mammals

Supplementary Table S1-S6 for PTMoreR

Table S1. The 115,179 and 42,997 phosphorylation sites (P-sites) for human and mouse phosphoproteomes obtained from two recent large-scale studies (1,2). Two sheet names here are marked as "Human.identified" and "Mouse.identified" respectively.

Table S2. The information and organism identifies for the 129 mammalian species downloaded from UniProt (http://www.uniprot.org/) (3).

Table S3. The phosphorylation expression data and statistical results from 10 common mammalian species (Euarchontoglires (i.e., Human, Rat, Rabbit, Monkey) and Laurasiatheria (i.e., Cow, Horse, Pig, Dog, Cat, Sheep)) (4).

Table S4. The features and the detectability matrix of P-sites in the Human.identified phosphoproteome data across species. Column 1 to 3 are UniProt ID, residue, and P-site position, respectively. Column 4 to 17 are the annotated phosphoproteome features that used in the Figure 2C, Figure 4B, 4E, 4F, Supplementary Figure S4 and S7B-S7C. Column 18 to 146 are the detectability matrix, in which the values are 0 for those sites not mapped in corresponding species and 1 for those mapped. The window similarity scores are >= 8.

Table S5. The GO terms with the BH adjusted P value < 0.01 in one of Q1-Q5 segments and > 0.05 in the other four from the GO enrichment analysis based on corresponding phosphoproteins.

Table S6. The results with BH adjusted P value < 0.01 from the kinase enrichment analysis in each of Q1-Q5 segments.

References

1.     Giansanti, P., Samaras, P., Bian, Y., Meng, C., Coluccio, A., Frejno, M., Jakubowsky, H., Dobiasch, S., Hazarika, R.R., Rechenberger, J. et al. (2022) Mass spectrometry-based draft of the mouse proteome. Nat Methods, 19, 803-811.

2.     Ochoa, D., Jarnuczak, A.F., Vieitez, C., Gehre, M., Soucheray, M., Mateus, A., Kleefeldt, A.A., Hill, A., Garcia-Alonso, L., Stein, F. et al. (2020) The functional landscape of the human phosphoproteome. Nat Biotechnol, 38, 365-373.

3.     UniProt, C. (2021) UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res, 49, D480-D489.

4.     Ba, Q., Hei, Y., Dighe, A., Li, W., Maziarz, J., Pak, I., Wang, S., Wagner, G.P. and Liu, Y. (2022) Proteotype coevolution and quantitative diversity across 11 mammalian species. Sci Adv, 8, eabn0756.