FluxFix: automatic isotopologue normalization for metabolic tracer analysis

Background Isotopic tracer analysis by mass spectrometry is a core technique for the study of metabolism. Isotopically labeled atoms from substrates, such as [ 13 C]-labeled glucose, can be traced by their incorporation over time into specific metabolic products. Mass spectrometry is often used for...

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Vydané v:BMC bioinformatics Ročník 17; číslo 1; s. 485
Hlavní autori: Trefely, Sophie, Ashwell, Peter, Snyder, Nathaniel W.
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: London BioMed Central 25.11.2016
BioMed Central Ltd
Springer Nature B.V
Predmet:
Algorithms
Bioinformatics
Biomarkers, Tumor - metabolism
Biomedical and Life Sciences
Carbon Isotopes - analysis
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
HeLa Cells
Hep G2 Cells
Humans
Isotope Labeling
Isotopic tracers
Life Sciences
Mass spectrometry
Mass Spectrometry - methods
Metabolites
Metabolomics
Metabolomics - methods
Methods
Microarrays
Results and data
Software
Trace analysis
Enrichment
Metabolite
Tracer
Flux
Normalization
Correction
Isotopologue
ISSN:1471-2105, 1471-2105
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Popis
Shrnutí:Background Isotopic tracer analysis by mass spectrometry is a core technique for the study of metabolism. Isotopically labeled atoms from substrates, such as [ 13 C]-labeled glucose, can be traced by their incorporation over time into specific metabolic products. Mass spectrometry is often used for the detection and differentiation of the isotopologues of each metabolite of interest. For meaningful interpretation, mass spectrometry data from metabolic tracer experiments must be corrected to account for the naturally occurring isotopologue distribution. The calculations required for this correction are time consuming and error prone and existing programs are often platform specific, non-intuitive, commercially licensed and/or limited in accuracy by using theoretical isotopologue distributions, which are prone to artifacts from noise or unresolved interfering signals. Results Here we present FluxFix ( http://fluxfix.science ), an application freely available on the internet that quickly and reliably transforms signal intensity values into percent mole enrichment for each isotopologue measured. ‘Unlabeled’ data, representing the measured natural isotopologue distribution for a chosen analyte, is entered by the user. This data is used to generate a correction matrix according to a well-established algorithm. The correction matrix is applied to labeled data, also entered by the user, thus generating the corrected output data. FluxFix is compatible with direct copy and paste from spreadsheet applications including Excel (Microsoft) and Google sheets and automatically adjusts to account for input data dimensions. The program is simple, easy to use, agnostic to the mass spectrometry platform, generalizable to known or unknown metabolites, and can take input data from either a theoretical natural isotopologue distribution or an experimentally measured one. Conclusions Our freely available web-based calculator, FluxFix ( http://fluxfix.science ), quickly and reliably corrects metabolic tracer data for natural isotopologue abundance enabling faster, more robust and easily accessible data analysis.
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ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-016-1360-7