'Isotopo' a database application for facile analysis and management of mass isotopomer data

Autor(en): Ahmed, Z.
Zeeshan, S.
Huber, C.
Hensel, M. 
Schomburg, D.
Münch, R.
Eylert, E.
Eisenreich, W.
Dandekar, T.
Stichwörter: bacterium; biology; chemistry; computer interface; computer program; data base; factual database; Internet; isotope labeling; mass spectrometry; metabolism; metabolome; procedures; Bacteria, Bacteria; Computational Biology; Database Management Systems; Databases, Factual; Internet; Isotope Labeling; Mass Spectrometry; Metabolome; Software; User-Computer Interface
Erscheinungsdatum: 2014
Journal: Database : the journal of biological databases and curation
Volumen: 2014
Zusammenfassung: 
UNLABELLED: The composition of stable-isotope labelled isotopologues/isotopomers in metabolic products can be measured by mass spectrometry and supports the analysis of pathways and fluxes. As a prerequisite, the original mass spectra have to be processed, managed and stored to rapidly calculate, analyse and compare isotopomer enrichments to study, for instance, bacterial metabolism in infection. For such applications, we provide here the database application 'Isotopo'. This software package includes (i) a database to store and process isotopomer data, (ii) a parser to upload and translate different data formats for such data and (iii) an improved application to process and convert signal intensities from mass spectra of (13)C-labelled metabolites such as tertbutyldimethylsilyl-derivatives of amino acids. Relative mass intensities and isotopomer distributions are calculated applying a partial least square method with iterative refinement for high precision data. The data output includes formats such as graphs for overall enrichments in amino acids. The package is user-friendly for easy and robust data management of multiple experiments. AVAILABILITY: The 'Isotopo' software is available at the following web link (section Download): http://spp1316.uni-wuerzburg.de/bioinformatics/isotopo/. The package contains three additional files: software executable setup (installer), one data set file (discussed in this article) and one excel file (which can be used to convert data from excel to '.iso' format). The 'Isotopo' software is compatible only with the Microsoft Windows operating system. DATABASE URL: http://spp1316.uni-wuerzburg.de/bioinformatics/isotopo/. © The Author(s) 2014. Published by Oxford University Press.
ISSN: 17580463
DOI: 10.1093/database/bau077
Externe URL: https://www.scopus.com/inward/record.uri?eid=2-s2.0-84925546414&doi=10.1093%2fdatabase%2fbau077&partnerID=40&md5=04348cbfea0bad8d223a248b5663a3a1

Show full item record

Page view(s)

5
Last Week
0
Last month
3
checked on May 23, 2024

Google ScholarTM

Check

Altmetric