title: Local database and the search program for proteomic analysis of sperm proteins in the ascidian Ciona intestinalis.
abstract: Separation of proteins by two-dimensional electrophoresis and following mass spectrometry (MS) is now a conventional technique for proteomic analysis. For proteomic analysis of a certain tissue with a limited information of primary structures of proteins, we have developed an analytical system for peptide mass fingerprinting in gene products in the testis of the ascidian Ciona intestinalis. Ciona sperm proteins were separated by two-dimensional gel electrophoresis and the tryptic fragments were subjected to MALDI-TOF/MS. The mass pattern was searched against on-line databases but resulted in less identification of these proteins. We have constructed a MS database from Ciona testis ESTs and the genome draft sequence, along with a newly devised, perl-based search program PerMS for peptide mass fingerprinting. This system could identify more than 80% of Ciona sperm proteins, suggesting that it could be widely applied for proteomic analysis for a limited tissue with less genomic information.
authors.affiliation: Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan.
authors.forename: Akiko
authors.initials: A
authors.lastname: Hozumi
authors.forename: Yuhkoh
authors.initials: Y
authors.lastname: Satouh
authors.forename: Daisuke
authors.initials: D
authors.lastname: Ishibe
authors.forename: Maiko
authors.initials: M
authors.lastname: Kaizu
authors.forename: Aru
authors.initials: A
authors.lastname: Konno
authors.forename: Yuji
authors.initials: Y
authors.lastname: Ushimaru
authors.forename: Tosifusa
authors.initials: T
authors.lastname: Toda
authors.forename: Kazuo
authors.initials: K
authors.lastname: Inaba
mesh_terms: D000818:Animals; D002938:Ciona intestinalis / Q000737:chemistry*; D030562:Databases, Protein; D015180:Electrophoresis, Gel, Two-Dimensional; D006801:Humans; D008297:Male; D013058:Mass Spectrometry; D010449:Peptide Mapping; D011506:Proteins / Q000032:analysis*; D020543:Proteome / Q000032:analysis*; D020539:Sequence Analysis, Protein; D013094:Spermatozoa / Q000737:chemistry*
chemical_list: D011506:Proteins; D020543:Proteome