Format

Send to

Choose Destination
Database (Oxford). 2014 Sep 9;2014. pii: bau077. doi: 10.1093/database/bau077. Print 2014.

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

Author information

1
Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Wuerzburg, Germany, Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany, Institute of Molecular and Translational Therapeutic Strategies, OE 8886, Hannover Medical School, Carl-Neuberg-Str. 1, D-30625 Hanover, Germany, Lehrstuhl für Biochemie, Center of Isotopologue Profiling, Lichtenbergstraße 4, Technische Universität München, D-85747 Garching, Germany, Division of Microbiology, Barbarastraße 11, Gebäude 36, University of Osnabrück, 49076 Osnabrück, Germany, Department of Bioinformatics and Biochemistry, Langer Kamp 19B, Technical University Braunschweig, D-38106 Braunschweig, Germany, Institute for Microbiology, Biozentrum, 2. Obergeschoss Spielmannstraße 7, Technical University Braunschweig, 38106 Braunschweig, Germany and Computational biology and structures program, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Wuerzburg, Germany, Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany, Institute of Molecular and Translational Therapeutic Strategies, OE 8886, Hannover Medical School, Carl-Neuberg-Str. 1, D-30625 Hanover, Germany, Lehrstuhl für Biochemie, Center of Isotopologue Profiling, Lichtenbergstraße 4, Technische Universität München, D-85747 Garching, Germany, Division of Microbiology, Barbarastraße 11, Gebäude 36, University of Osnabrück, 49076 Osnabrück, Germany, Department of Bioinformatics and Biochemistry, Langer Kamp 19B, Technical University Braunschweig, D-38106 Braunschweig, Germany, Institute for Microbiology, Biozentrum, 2. Obergeschoss Spielmannstraße 7, Technical University Braunschweig, 38106 Braunschweig, Germany and Computational biology and structures program, European Molecular Biology Laboratory, Meye
2
Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Wuerzburg, Germany, Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany, Institute of Molecular and Translational Therapeutic Strategies, OE 8886, Hannover Medical School, Carl-Neuberg-Str. 1, D-30625 Hanover, Germany, Lehrstuhl für Biochemie, Center of Isotopologue Profiling, Lichtenbergstraße 4, Technische Universität München, D-85747 Garching, Germany, Division of Microbiology, Barbarastraße 11, Gebäude 36, University of Osnabrück, 49076 Osnabrück, Germany, Department of Bioinformatics and Biochemistry, Langer Kamp 19B, Technical University Braunschweig, D-38106 Braunschweig, Germany, Institute for Microbiology, Biozentrum, 2. Obergeschoss Spielmannstraße 7, Technical University Braunschweig, 38106 Braunschweig, Germany and Computational biology and structures program, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany.

Abstract

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/.

PMID:
25204646
PMCID:
PMC4158277
DOI:
10.1093/database/bau077
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center