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Isotope Calculation Gadgets: A Series of Software for Isotope-Tracing Experiments in Garuda Platform

2022; Multidisciplinary Digital Publishing Institute; Volume: 12; Issue: 7 Linguagem: Inglês

10.3390/metabo12070646

2218-1989

Nobuyuki Okahashi, Yuki Yamada, Junko Iida, Fumio Matsuda,

Microbial Metabolic Engineering and Bioproduction

Isotope tracing is a powerful technique for elucidating intracellular metabolism. Experiments utilizing this technique involve various processes, such as the correction of natural isotopes. Although some previously developed software are available for these procedures, there are still time-consuming steps in isotope tracing including the creation of an isotope measurement method in mass spectrometry (MS) and the interpretation of obtained labeling data. Additionally, these multi-step tasks often require data format conversion, which is also time-consuming. In this study, the Isotope Calculation Gadgets, a series of software that supports an entire workflow of isotope-tracing experiments, was developed in the Garuda platform, an open community. Garuda is a graphical user interface-based platform that allows individual operations to be sequentially performed, without data format conversion, which significantly reduces the required time and effort. The developed software includes new features that construct channels for isotopomer measurements, as well as conventional functions such as natural isotope correction, the calculation of fractional labeling and split ratio, and data mapping, thus facilitating an overall workflow of isotope-tracing experiments through smooth functional integration.