Cuban scientists have allowed free access
to the software Isotopica for Proteomics
José A.
Acosta ,
Ricardo S. Rodríguez, Boris E. Acevedo
Havana - November 28.
The Center for Genetic Engineering and Biotec hnology (CIGB) from
Havana , Cuba , has announced today the release of the software "Isotopica" for
research in the field of Proteomics. Isotopica is a web application,
the server can be accessed at http://bioinformatica.cigb.edu.cu and
it offers free access to the following services:
• Matching compounds to raw spectrum.
• Simulator of isotopic envelope.
• Element table and residue library.
• Residue registration.
• File converter for Isotopica viewer.
• Element isotope abundance registration.
• Digest for peptide mass fingerprint.
• Formula calculator.
Isotopica allows for 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 bio molecules, which are often subjected to additional modifications
other than normal constituents, such as post-translational modification
in proteins. The results also can be displayed graphically on a
local PC using the Isotopica viewer, a standalone application that
is downloadable from the same web site as a complement to the client
browser. This application is useful for validating an observed
peak alongside the theoretical one, especially one with a higher
mass or a complex pattern due to the presence of more than two
components or enriched stable isotopes within the isotopic distribution.
The mass/charge 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. This software can be useful
not only for validating the purity of an analytic compound, but
also for constructing an in silico Mass Spectrometry
(MS) spectrum based on the given abundances of each component in
a mixture.
MS, an essential tool for proteomic analysis, allows the prompt
identification of proteins in conjunction with a sequence database
search. Since the performance of MS has been significantly improved
with respect to resolution and accuracy, complex and high-molecular-weight
biopolymers such as glycoproteins can now be analyzed. In order
to support the calculation of the mass and theoretical isotopic
distribution of a mixture of complex biopolymers, Isotopica permits
flexible input of multiple components, based on protein sequence,
molecular formulas, and so on.
About the CIGB
The CIGB, a vanguard institution in the Life Sciences
in Cuba , is a large research-production complex, endowed with
the state of the art equipment, production capacities and personnel
devoted to the development of new biotechnology products in all
stages, from the cloning and expression using recombinant DNA technology
to industrial production. The CIGB has extensive experience in
the recombinant DNA technology dated back to 1980, with more than
1300 employees, owning the most modern and efficient technology,
carefully studied-beforehand facilities so as to ease the quiet
and continuous workflow with a total area of more than 70 000 m².
For information: http://gndp.cigb.edu.cu or http://www.cigb.edu.cu
Contact: ricardo.silva@cigb.edu.cu
Phone: (53-7) 2712397. |
