The ProteomeXchange consortium at 10 years: 2023 update

“…Per2 gene showed a marked signature of diversifying selection around the site 263 in the alignment ( Supplementary Fig. 4 , Supplementary Table 6 ), while we did not find known functional annotation there but “Polar residues, Compositional bias” in Uniprot (corresponding with the 46th “N” in NENCS in the human sequence, O15055 · PER2_HUMAN at UNIProt, https://www.uniprot.org/uniprotkb/O15055/entry , last accessed, July 3 2023 ( Deutsch et al 2023 )).…”

“…The site under selection in CRY-binding region is conserved, but after that, the latter binding region shows a dramatic decline in conservation ( Fig 5A and 5B) , which may indicate sub-functionalization between paralogs, and the molecular basis of functional diversification of Per genes between species. Per2 gene showed a marked signature of diversifying selection around the site 263 in the alignment ( Fig S4, TableS6), while we did not find known functional annotation there but “Polar residues, Compositional bias” in Uniprot (corresponding with the 46th “N” in NE N CS in the human sequence, O15055 · PER2_HUMAN at UNIProt, https://www.uniprot.org/uniprotkb/O15055/entry, last accessed, July 3 rd 2023 (Deutsch et al 2023).…”

“…Models generated with such parameters were used as a search database for matching MS peptides present in 16 biological samples generated by three studies (Marx et al, 2016; Shin et al, 2021; Castañeda et al, 2021). Corresponding MS proteomic data were downloaded from PreoteomeXchange (Vizcaíno et al, 2014; Deutsch et al, 2023). The MS searches were conducted independently for models based on conserved and MS-supported altORFs.…”