Christian Jungreuthmayer1, Stefan Neubauer2, Teresa Mairinger2, Jürgen Zanghellini1, Stephan Hann2. 1. Austrian Centre of Industrial Biotechnology (ACIB), Vienna, Austria, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria and. 2. Austrian Centre of Industrial Biotechnology (ACIB), Vienna, Austria, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria.
Abstract
SUMMARY: Isotope tracer experiments are an invaluable technique to analyze and study the metabolism of biological systems. However, isotope labeling experiments are often affected by naturally abundant isotopes especially in cases where mass spectrometric methods make use of derivatization. The correction of these additive interferences--in particular for complex isotopic systems--is numerically challenging and still an emerging field of research. When positional information is generated via collision-induced dissociation, even more complex calculations for isotopic interference correction are necessary. So far, no freely available tools can handle tandem mass spectrometry data. We present isotope correction toolbox, a program that corrects tandem mass isotopomer data from tandem mass spectrometry experiments. Isotope correction toolbox is written in the multi-platform programming language Perl and, therefore, can be used on all commonly available computer platforms. AVAILABILITY AND IMPLEMENTATION: Source code and documentation can be freely obtained under the Artistic License or the GNU General Public License from: https://github.com/jungreuc/isotope_correction_toolbox/ CONTACT: {christian.jungreuthmayer@boku.ac.at,juergen.zanghellini@boku.ac.at} SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: Isotope tracer experiments are an invaluable technique to analyze and study the metabolism of biological systems. However, isotope labeling experiments are often affected by naturally abundant isotopes especially in cases where mass spectrometric methods make use of derivatization. The correction of these additive interferences--in particular for complex isotopic systems--is numerically challenging and still an emerging field of research. When positional information is generated via collision-induced dissociation, even more complex calculations for isotopic interference correction are necessary. So far, no freely available tools can handle tandem mass spectrometry data. We present isotope correction toolbox, a program that corrects tandem mass isotopomer data from tandem mass spectrometry experiments. Isotope correction toolbox is written in the multi-platform programming language Perl and, therefore, can be used on all commonly available computer platforms. AVAILABILITY AND IMPLEMENTATION: Source code and documentation can be freely obtained under the Artistic License or the GNU General Public License from: https://github.com/jungreuc/isotope_correction_toolbox/ CONTACT: {christian.jungreuthmayer@boku.ac.at,juergen.zanghellini@boku.ac.at} SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Lina Heistinger; Juliane C Dohm; Barbara G Paes; Daniel Koizar; Christina Troyer; Özge Ata; Teresa Steininger-Mairinger; Diethard Mattanovich Journal: Microb Cell Fact Date: 2022-04-25 Impact factor: 6.352
Authors: Paul Heinrich; Christian Kohler; Lisa Ellmann; Paul Kuerner; Rainer Spang; Peter J Oefner; Katja Dettmer Journal: Sci Rep Date: 2018-12-17 Impact factor: 4.379