title: Isotopica: a tool for the calculation and viewing of complex isotopic envelopes.
abstract: The web application Isotopica has been developed as an aid to the interpretation of ions that contain naturally occurring isotopes in a mass spectrum. It allows the calculation of mass values and isotopic distributions based on molecular formulas, peptides/proteins, DNA/RNA, carbohydrate sequences or combinations thereof. In addition, Isotopica takes modifications of the input molecule into consideration using a simple and flexible language as a straightforward extension of the molecular formula syntax. This function is especially useful for biomolecules, which are often subjected to additional modifications other than normal constituents, such as the frequently occurring post-translational modification in proteins. The isotopic distribution of any molecule thus defined can be calculated by considering full widths at half maximum or mass resolution. The combined envelope of several overlapping isotopic distributions of a mixture of molecules can be determined after specifying each molecule's relative abundance. The results can be displayed graphically on a local PC using the Isotopica viewer, a standalone application that is downloadable from the sites below, as a complement to the client browser. The m/z and intensity values can also be obtained in the form of a plain ASCII text file. The software has proved to be useful for peptide mass fingerprinting and validating an observed isotopic ion distribution with reference to the theoretical one, even from a multi-component sample. The web server can be accessed at http://bioinformatica.cigb.edu.cu/isotopica and http://coco.protein.osaka-u.ac.jp/isotopica [correction].
authors.affiliation: Center for Genetic Engineering and Biotechnology, P.O. Box 6162, Havana, Cuba. jorge.cossio@cigb.edu.cu
authors.forename: Jorge
authors.initials: J
authors.lastname: Fernandez-de-Cossio
authors.forename: Luis Javier
authors.initials: LJ
authors.lastname: Gonzalez
authors.forename: Yoshinori
authors.initials: Y
authors.lastname: Satomi
authors.forename: Lazaro
authors.initials: L
authors.lastname: Betancourt
authors.forename: Yassel
authors.initials: Y
authors.lastname: Ramos
authors.forename: Vivian
authors.initials: V
authors.lastname: Huerta
authors.forename: Abel
authors.initials: A
authors.lastname: Amaro
authors.forename: Vladimir
authors.initials: V
authors.lastname: Besada
authors.forename: Gabriel
authors.initials: G
authors.lastname: Padron
authors.forename: Naoto
authors.initials: N
authors.lastname: Minamino
authors.forename: Toshifumi
authors.initials: T
authors.lastname: Takao
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D001704:Biopolymers / Q000737:chemistry; D002240:Carbohydrate Sequence; D003196:Computer Graphics; D020407:Internet; D007477:Ions / Q000737:chemistry; D007554:Isotopes / Q000032:analysis*; D013058:Mass Spectrometry; D008432:Mathematical Computing; D010449:Peptide Mapping; D012984:Software; D014584:User-Computer Interface
chemical_list: D001704:Biopolymers; D007477:Ions; D007554:Isotopes