Please use this identifier to cite or link to this item: http://hdl.handle.net/2445/112072
Title: MIDcor, an R-program for deciphering mass interferences in mass spectra of metabolites enriched in stable isotopes
Author: Selivanov, Vitaly A.
Benito Mauricio, Adrián
Miranda, Aníbal
Aguilar Fadó, Esther
Polat, Ibrahim Halil
Centelles Serra, Josep Joan
Jayaraman, Anusha
Lee, Paul W.
Marín Martínez, Silvia
Cascante i Serratosa, Marta
Keywords: Cromatografia de gasos
Espectrometria de masses
Cèl·lules
Metabolisme
Isòtops
Gas chromatography
Mass spectrometry
Cells
Metabolism
Isotopes
Issue Date: 3-Feb-2017
Publisher: BioMed Central
Abstract: Background: Tracing stable isotopes, such as 13 C using various mass spectrometry (MS) methods provides a valuable information necessary for the study of biochemical processes in cells. However, extracting such information requires special care, such as a correction for naturally occurring isotopes, or overlapping mass spectra of various components of the cell culture medium. Developing a method for a correction of overlapping peaks is the primary objective of this study. Results: Our computer program-MIDcor (free at https://github.com/seliv55/mid_correct) written in the R programming language, corrects the raw MS spectra both for the naturally occurring isotopes and for the overlapping of peaks corresponding to various substances. To this end, the mass spectra of unlabeled metabolites measured in two media are necessary: in a minimal medium containing only derivatized metabolites and chemicals for derivatization, and in a complete cell incubated medium. The MIDcor program calculates the difference (D)between the theoretical and experimentally measured spectra of metabolites containing only the naturally occurring isotopes. The result of comparison of D in the two media determines a way of deciphering the true spectra. (1) If D in the complete medium is greater than that in the minimal medium in at least one peak, then unchanged D is subtracted from the raw spectra of the labeled metabolite. (2) If D does not depend on the medium, then the spectrum probably overlaps with a derivatized fragment of the same metabolite, and D is modified proportionally to the metabolite labeling. The program automatically reaches a decision regarding the way of correction. For some metabolites/fragments in the case (2)D was found to decrease when the tested substance was 13 C labeled, and this isotopic effect also can be corrected automatically, if the user provides a measured spectrum of the substance in which the 13 C labeling is known a priori. Conclusion: Using the developed program improves the reliability of stable isotope tracer data analysis.
Note: Reproducció del document publicat a: https://doi.org/10.1186/s12859-017-1513-3
It is part of: BMC Bioinformatics, 2017, vol. 18, num. 1, p. 88
Related resource: https://doi.org/10.1186/s12859-017-1513-3
URI: http://hdl.handle.net/2445/112072
ISSN: 1471-2105
Appears in Collections:Articles publicats en revistes (Bioquímica i Biomedicina Molecular)

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