Introduction

Tracing stable isotopes, such as 13C 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.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 13C labeled, and this isotopic effect also can be corrected automatically, if the user provides a measured spectrum of the substance in which the 13C labeling is known a priori.Using the developed program improves the reliability of stable isotope tracer data analysis.

Publications

  1. MIDcor, an R-program for deciphering mass interferences in mass spectra of metabolites enriched in stable isotopes.
    Cite this
    Selivanov VA, Benito A, Miranda A, Aguilar E, Polat IH, Centelles JJ, Jayaraman A, Lee PW, Marin S, Cascante M, 2017-02-01 - BMC bioinformatics

Credits

  1. Vitaly A Selivanov
    Developer

    Institute of Biomedicine of the Universitat de Barcelona (IBUB) and Associated Unit to CSIC, Barcelona, Spain

  2. Adrián Benito
    Developer

    Institute of Biomedicine of the Universitat de Barcelona (IBUB) and Associated Unit to CSIC, Barcelona, Spain

  3. Anibal Miranda
    Developer

    Institute of Biomedicine of the Universitat de Barcelona (IBUB) and Associated Unit to CSIC, Barcelona, Spain

  4. Esther Aguilar
    Developer

    Institute of Biomedicine of the Universitat de Barcelona (IBUB) and Associated Unit to CSIC, Barcelona, Spain

  5. Ibrahim Halil Polat
    Developer

    Institute of Biomedicine of the Universitat de Barcelona (IBUB) and Associated Unit to CSIC, Barcelona, Spain

  6. Josep J Centelles
    Developer

    Institute of Biomedicine of the Universitat de Barcelona (IBUB) and Associated Unit to CSIC, Barcelona, Spain

  7. Anusha Jayaraman
    Developer

    Institute of Biomedicine of the Universitat de Barcelona (IBUB) and Associated Unit to CSIC, Barcelona, Spain

  8. Paul W N Lee
    Developer

    Department of Pediatrics, Harbor-UCLA Medical Center, United States of America

  9. Silvia Marin
    Developer

    Institute of Biomedicine of the Universitat de Barcelona (IBUB) and Associated Unit to CSIC, Barcelona, Spain

  10. Marta Cascante
    Investigator

    Institute of Biomedicine of the Universitat de Barcelona (IBUB) and Associated Unit to CSIC, Barcelona, Spain

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT001632
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Country/RegionSpain
Submitted ByMarta Cascante