TY - JOUR
T1 - 'Isotopo' a database application for facile analysis and management of mass isotopomer data
AU - Ahmed, Zeeshan
AU - Zeeshan, Saman
AU - Huber, Claudia
AU - Hensel, Michael
AU - Schomburg, Dietmar
AU - Münch, Richard
AU - Eylert, Eva
AU - Eisenreich, Wolfgang
AU - Dandekar, Thomas
N1 - Publisher Copyright:
© The Author(s) 2014. Published by Oxford University Press.
PY - 2014
Y1 - 2014
N2 - 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/.
AB - 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/.
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U2 - 10.1093/database/bau077
DO - 10.1093/database/bau077
M3 - Article
C2 - 25204646
AN - SCOPUS:84925546414
SN - 1758-0463
VL - 2014
JO - Database : the journal of biological databases and curation
JF - Database : the journal of biological databases and curation
ER -