Isotopomer distribution computation from tandem mass spectrometric data with overlapping fragment spectra

Juho Rousu, Ari Rantanen, Raimo A. Ketola, Juha T. Kokkonen

Research output: Contribution to journalArticleScientificpeer-review

9 Citations (Scopus)

Abstract

We present a method for determination of the isotopomer distributions of metabolites from the data generated by a tandem mass spectrometer. The method is an improvement over existing method as it is able to deal with overlapping fragments in the spectra. Our experiments indicate that the new method surpasses its predecessors in separating isotopomers from each other. When using the daughter ion scanning (collision induced dissociation) mode, the method was shown to be able to constrain the isotopomer distribution of different amino acids better than two existing methods. In particular, the isotopomer distributions of three amino acids, glycine, alanine and serine, can be fully uncovered with the method. However, due to the imperfect fragmentation of molecules in the tandem mass spectrometer, isotopomer distributions of larger amino acids still cannot be fully uncovered. In tests with isotope‐labelled alanine, most accurate results were obtained using multiple reaction monitoring and 15 eV collision energy. The meausured isotopomer frequecies were in the range 99–106% of the theoretical value and the deviation between repetitions was in the range 1–10%.
Original languageEnglish
Pages (from-to)53 - 67
Number of pages15
JournalSpectroscopy
Volume19
Issue number1
DOIs
Publication statusPublished - 2005
MoE publication typeA1 Journal article-refereed

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Mass spectrometers
Amino Acids
Alanine
Metabolites
Glycine
Serine
Ions
Scanning
Molecules
Monitoring
Experiments

Cite this

Rousu, Juho ; Rantanen, Ari ; Ketola, Raimo A. ; Kokkonen, Juha T. / Isotopomer distribution computation from tandem mass spectrometric data with overlapping fragment spectra. In: Spectroscopy. 2005 ; Vol. 19, No. 1. pp. 53 - 67.
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abstract = "We present a method for determination of the isotopomer distributions of metabolites from the data generated by a tandem mass spectrometer. The method is an improvement over existing method as it is able to deal with overlapping fragments in the spectra. Our experiments indicate that the new method surpasses its predecessors in separating isotopomers from each other. When using the daughter ion scanning (collision induced dissociation) mode, the method was shown to be able to constrain the isotopomer distribution of different amino acids better than two existing methods. In particular, the isotopomer distributions of three amino acids, glycine, alanine and serine, can be fully uncovered with the method. However, due to the imperfect fragmentation of molecules in the tandem mass spectrometer, isotopomer distributions of larger amino acids still cannot be fully uncovered. In tests with isotope‐labelled alanine, most accurate results were obtained using multiple reaction monitoring and 15 eV collision energy. The meausured isotopomer frequecies were in the range 99–106{\%} of the theoretical value and the deviation between repetitions was in the range 1–10{\%}.",
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Isotopomer distribution computation from tandem mass spectrometric data with overlapping fragment spectra. / Rousu, Juho; Rantanen, Ari; Ketola, Raimo A.; Kokkonen, Juha T.

In: Spectroscopy, Vol. 19, No. 1, 2005, p. 53 - 67.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - Isotopomer distribution computation from tandem mass spectrometric data with overlapping fragment spectra

AU - Rousu, Juho

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AU - Kokkonen, Juha T.

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N2 - We present a method for determination of the isotopomer distributions of metabolites from the data generated by a tandem mass spectrometer. The method is an improvement over existing method as it is able to deal with overlapping fragments in the spectra. Our experiments indicate that the new method surpasses its predecessors in separating isotopomers from each other. When using the daughter ion scanning (collision induced dissociation) mode, the method was shown to be able to constrain the isotopomer distribution of different amino acids better than two existing methods. In particular, the isotopomer distributions of three amino acids, glycine, alanine and serine, can be fully uncovered with the method. However, due to the imperfect fragmentation of molecules in the tandem mass spectrometer, isotopomer distributions of larger amino acids still cannot be fully uncovered. In tests with isotope‐labelled alanine, most accurate results were obtained using multiple reaction monitoring and 15 eV collision energy. The meausured isotopomer frequecies were in the range 99–106% of the theoretical value and the deviation between repetitions was in the range 1–10%.

AB - We present a method for determination of the isotopomer distributions of metabolites from the data generated by a tandem mass spectrometer. The method is an improvement over existing method as it is able to deal with overlapping fragments in the spectra. Our experiments indicate that the new method surpasses its predecessors in separating isotopomers from each other. When using the daughter ion scanning (collision induced dissociation) mode, the method was shown to be able to constrain the isotopomer distribution of different amino acids better than two existing methods. In particular, the isotopomer distributions of three amino acids, glycine, alanine and serine, can be fully uncovered with the method. However, due to the imperfect fragmentation of molecules in the tandem mass spectrometer, isotopomer distributions of larger amino acids still cannot be fully uncovered. In tests with isotope‐labelled alanine, most accurate results were obtained using multiple reaction monitoring and 15 eV collision energy. The meausured isotopomer frequecies were in the range 99–106% of the theoretical value and the deviation between repetitions was in the range 1–10%.

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