title: Iterative genome correction largely improves proteomic analysis of nonmodel organisms.
abstract: 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.
authors.affiliation: Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , Huang-Pu Avenue West 601, Guangzhou 510632, China.
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Wu
authors.forename: Lina
authors.initials: L
authors.lastname: Xu
authors.forename: Wei
authors.initials: W
authors.lastname: Gu
authors.forename: Qian
authors.initials: Q
authors.lastname: Xu
authors.forename: Qing-Yu
authors.initials: QY
authors.lastname: He
authors.forename: Xuesong
authors.initials: X
authors.lastname: Sun
authors.forename: Gong
authors.initials: G
authors.lastname: Zhang
mesh_terms: D000595:Amino Acid Sequence; D001407:Bacillus / Q000235:genetics*; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics*; D001483:Base Sequence; D030562:Databases, Protein; D014644:Genetic Variation; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry; D010449:Peptide Mapping; D020543:Proteome / Q000737:chemistry / Q000235:genetics*; D040901:Proteomics; D017422:Sequence Analysis, DNA; D053719:Tandem Mass Spectrometry
chemical_list: D001426:Bacterial Proteins; D010446:Peptide Fragments; D020543:Proteome