MIDcor, an R-program for deciphering mass interferences in mass spectra of metabolites enriched in stable isotopes. Issue 1 (December 2017)

• Record Type: Journal Article
• Authors: Selivanov, Vitaly; Benito, Adrián; Miranda, Anibal; Aguilar, Esther; Polat, Ibrahim; Centelles, Josep; Jayaraman, Anusha; Lee, Paul; Marin, Silvia; Cascante, Marta
• Is Part Of: BMC bioinformatics. Volume 18:Issue 1(2017)
• Page Start: 1
• Page End: 9
• Publication Date: 2017-12
• Subjects: 13C labeling of metabolites -- Gas chromatography/mass spectrometry -- Correction of peaks overlapping -- Isotopic effect -- Computational analysis -- R-program; Bioinformatics -- Periodicals; Computational biology -- Periodicals; 570.285
• DOI: 10.1186/s12859-017-1513-3
• Languages: English
• ISSNs: 1471-2105

Abstract

Abstract Background Tracing stable isotopes, such as13 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 athttps://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 ofD in the two media determines a way of deciphering the true spectra. (1) IfD in the complete medium is greater than that in the minimal medium in at least one peak, then unchangedD is subtracted from the raw spectra of the labeled metabolite. (2) IfD does not depend on the medium, then the spectrum probably overlaps with a derivatized fragment of the same metabolite, andD 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 was13 C labeled, and this isotopic effect also can be corrected automatically, if the user provides a measured spectrum of the substance in which the13 C labeling is known a priori. Conclusion Using the developed program improves the reliability of stable isotope tracer data analysis.