customized protein database

The protein database included a metagenome-derived protein database (metagenomic DB), a rumen microbial database (rumen DB) , and bacterial database from reviewed Swiss-Prot (Swiss-Prot DB). The metagenome-derived protein database was constructed based on rumen fluid samples from dairy goats. The customized database was conducted by a two-step database search. Briefly, the raw MS/MS spectra were searched against the metagenomic DB, rumen DB, and Swiss-Prot DB, in which parameters of unique peptide,−10 lgP and FDR were set to 0. All proteins identified from each database were merged and deduplicated using CD-HIT (v.4.8.1)to create a new customized database.