title: Efficiency improvement of peptide identification for an organism without complete genome sequence, using expressed sequence tag database and tandem mass spectral data.
abstract: We compared peptide identification by database (DB) search methods with de novo sequencing results for proteomics study in an organism without genome sequence information. When the former was done by searching the Expressed Sequence Tag (EST) DB of the sample organism or the NCBI nonredundant (nr) protein DB of green plants using either the MASCOT or SEQUEST software program, it was confirmed that the former is as accurate as the latter. Peptides identified from EST DB were twice as many as those from the nr protein DB, in spite of the fact that the EST DB has less data (26 222 EST) than the NCBI nr protein DB (224 238). This study demonstrates that EST DB with tandem mass spectra can be used reliably for high-throughput proteomics studies in an organism without genome information.
authors.affiliation: Korea Basic Science Institute, 52 Yeo-Eun Dong, Yusung-gu, Daejeon 305-333, Korea.
authors.forename: Kyung-Hoon
authors.initials: KH
authors.lastname: Kwon
authors.forename: Mioak
authors.initials: M
authors.lastname: Kim
authors.forename: Jin Young
authors.initials: JY
authors.lastname: Kim
authors.forename: Kyung Wook
authors.initials: KW
authors.lastname: Kim
authors.forename: Seung Il
authors.initials: SI
authors.lastname: Kim
authors.forename: Young Mok
authors.initials: YM
authors.lastname: Park
authors.forename: Jong Shin
authors.initials: JS
authors.lastname: Yoo
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology; D030562:Databases, Protein; D020224:Expressed Sequence Tags; D016678:Genome; D008969:Molecular Sequence Data; D010455:Peptides / Q000235:genetics; D010944:Plants / Q000737:chemistry / Q000235:genetics*; D040901:Proteomics; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
chemical_list: D010455:Peptides