Iterative Genome Correction Largely Improves Proteomic Analysis of Nonmodel Organisms

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
nonmodel organisms. In this study, we demonstrated a new strategy
based on our stable, accurate, and error-tolerant FANSe (Fast and
Accurate mapping tool for Nucleotide Sequencing datasets) 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 nonmodel organisms.