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bioRxiv · 10.1101/2020.09.19.304741

Corna - An Open Source Python Tool For Natural Abundance Correction In Isotope Tracer Experiments

Raaisa, R.·Lathwal, S.·Chubukov, V.·Kibbey, R. G.·Jha, A. K.
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Abstract

BackgroundStable isotope-based approaches are used in the field of metabolomics for quantification and identification of metabolites, discovery of new pathways and measurement of intracellular fluxes. In these experiments, often performed with mass spectrometry (MS), data must be corrected for natural abundance of isotopes. Various stand-alone tools with their own separate data formats and learning curves exist for correction of data collected at different resolutions, for tandem MS, and for different number of tracer elements. ResultsWe present a Python package, Corna, that combines natural abundance correction workflows for several experimental conditions and can be used as a one-stop-shop for stable isotope labeled experiments. We validate the algorithms in Corna with published tools, where available, and include new features, such as correction of two tracer elements, that are not yet implemented in any existing software application as per our knowledge. We also present the integration of Corna with an existing open source peak integration software. The integrated workflow can reduce processing times for a typical stable isotope based workflow from days to hours for a familiar user. ConclusionsAlgorithmic advancements have been keeping up with the developments in mass spectrometry technologies and have been the focus of most existing tools for natural abundance correction. However, in this high throughput era, it is also important to recognize user experience, and integrated and reproducible workflows. Corna has been written in Python and is designed for users who have access to large amounts of data from different kinds of experiments and want to integrate a natural abundance correction tool seamlessly in their pipelines. The latest version of Corna can be accessed at https://github.com/raaisakuk/NA_Correction.

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Raaisa, R., Lathwal, S., Chubukov, V., Kibbey, R. G., Jha, A. K.. 2020-09-20. Corna - An Open Source Python Tool For Natural Abundance Correction In Isotope Tracer Experiments. https://doi.org/10.1101/2020.09.19.304741

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