Computing positional isotopomer distributions from tandem mass spectrometric data

Ari Rantanen (Corresponding Author), Juho Rousu, Juha T. Kokkonen, Virpi Tarkiainen, Raimo A. Ketola

Research output: Contribution to journalArticleScientificpeer-review

21 Citations (Scopus)

Abstract

The isotopomer distributions of metabolites are invaluable pieces of information in the computation of the flux distribution in a metabolic network. We describe the use of tandem mass spectrometry with the daughter ion scanning technique in the discovery of positional isotopomer distributions (PID). This technique increases the possibilities of mass spectrometry since given same fragment ions, it uncovers more information than the full scanning mode. The mathematics of the new technique is slightly more complicated than the techniques needed by full scanning methods. Our experiments, however, show that in the practice the inadequancy of the fragmentation of amino acids in the tandem mass spectrometer does not allow uncovering the PID exactly even if the daughter ion scanning is used. The computational techniques have been implemented in a MATLAB appication called PIDC (Positional Isotopomer Distribution Calculator).
Original languageEnglish
Pages (from-to)285-294
JournalMetabolic Engineering
Volume4
Issue number4
DOIs
Publication statusPublished - 2002
MoE publication typeA1 Journal article-refereed

Fingerprint

Ions
Scanning
Mass spectrometry
Mathematics
Tandem Mass Spectrometry
Metabolic Networks and Pathways
Mass Spectrometry
Mass spectrometers
Metabolites
MATLAB
Amino acids
Amino Acids
Fluxes
Experiments

Keywords

  • flux analysis
  • isotopomer distribution
  • tandem mass spectrometry

Cite this

Rantanen, A., Rousu, J., Kokkonen, J. T., Tarkiainen, V., & Ketola, R. A. (2002). Computing positional isotopomer distributions from tandem mass spectrometric data. Metabolic Engineering, 4(4), 285-294. https://doi.org/10.1006/mben.2002.0232
Rantanen, Ari ; Rousu, Juho ; Kokkonen, Juha T. ; Tarkiainen, Virpi ; Ketola, Raimo A. / Computing positional isotopomer distributions from tandem mass spectrometric data. In: Metabolic Engineering. 2002 ; Vol. 4, No. 4. pp. 285-294.
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Rantanen, A, Rousu, J, Kokkonen, JT, Tarkiainen, V & Ketola, RA 2002, 'Computing positional isotopomer distributions from tandem mass spectrometric data', Metabolic Engineering, vol. 4, no. 4, pp. 285-294. https://doi.org/10.1006/mben.2002.0232

Computing positional isotopomer distributions from tandem mass spectrometric data. / Rantanen, Ari (Corresponding Author); Rousu, Juho; Kokkonen, Juha T.; Tarkiainen, Virpi; Ketola, Raimo A.

In: Metabolic Engineering, Vol. 4, No. 4, 2002, p. 285-294.

Research output: Contribution to journalArticleScientificpeer-review

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T1 - Computing positional isotopomer distributions from tandem mass spectrometric data

AU - Rantanen, Ari

AU - Rousu, Juho

AU - Kokkonen, Juha T.

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AU - Ketola, Raimo A.

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AB - The isotopomer distributions of metabolites are invaluable pieces of information in the computation of the flux distribution in a metabolic network. We describe the use of tandem mass spectrometry with the daughter ion scanning technique in the discovery of positional isotopomer distributions (PID). This technique increases the possibilities of mass spectrometry since given same fragment ions, it uncovers more information than the full scanning mode. The mathematics of the new technique is slightly more complicated than the techniques needed by full scanning methods. Our experiments, however, show that in the practice the inadequancy of the fragmentation of amino acids in the tandem mass spectrometer does not allow uncovering the PID exactly even if the daughter ion scanning is used. The computational techniques have been implemented in a MATLAB appication called PIDC (Positional Isotopomer Distribution Calculator).

KW - flux analysis

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KW - tandem mass spectrometry

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JO - Metabolic Engineering

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SN - 1096-7176

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