Bacillus pumilus (environmental isolate) Genome sequencing. Bacillus pumilus strain:JN01

The current application and development of proteomic studies typically depend on the availability of sequenced genomes. Protein identification based on the detected peptides with liquid chromatography tandem mass spectrometry is limited by the absence of sequenced genomes in many non-model organisms. In this study, we demonstrated a new strategy based on our stable, accurate and error-tolerant FANSe mapping algorithm to correct genome sequences in an iterative manner. To evaluate the efficiency of the corrected genome databases in proteomic study, MS/MS spectra of whole proteome extracted from a Bacillus pumilus strain without complete genome sequence were searched against the protein sequence databases derived from the complete reference genome sequence of a homologous bacterium and from the corrected genome sequence. The results indicated that the corrected protein sequence database could significantly facilitate peptide/protein identification. Importantly, this strategy can help to detect novel peptide variants. This strategy of genome correction will promote the development of functional proteomics in non-model organisms.