FiD

A software for ab initio structural identification of product ions from tandem mass spectrometric data

Markus Heinonen (Corresponding Author), Ari Rantanen, Taneli Mielikäinen, Juha Kokkonen, Jari Kiuru, Raimo A. Ketola, Juho Rousu

Research output: Contribution to journalArticleScientificpeer-review

79 Citations (Scopus)

Abstract

We present FiD (Fragment iDentificator), a software tool for the structural identification of product ions produced with tandem mass spectrometric measurement of low molecular weight organic compounds. Tandem mass spectrometry (MS/MS) has proven to be an indispensable tool in modern, cell‐wide metabolomics and fluxomics studies. In such studies, the structural information of the MSn product ions is usually needed in the downstream analysis of the measurement data. The manual identification of the structures of MSn product ions is, however, a nontrivial task requiring expertise, and calls for computer assistance. Commercial software tools, such as Mass Frontier and ACD/MS Fragmenter, rely on fragmentation rule databases for the identification of MSn product ions. FiD, on the other hand, conducts a combinatorial search over all possible fragmentation paths and outputs a ranked list of alternative structures. This gives the user an advantage in situations where the MS/MS data of compounds with less well‐known fragmentation mechanisms are processed. FiD software implements two fragmentation models, the single‐step model that ignores intermediate fragmentation states and the multi‐step model, which allows for complex fragmentation pathways. The software works for MS/MS data produced both in positive‐ and negative‐ion modes. The software has an easy‐to‐use graphical interface with built‐in visualization capabilities for structures of product ions and fragmentation pathways. In our experiments involving amino acids and sugar‐phosphates, often found, e.g., in the central carbon metabolism of yeasts, FiD software correctly predicted the structures of product ions on average in 85% of the cases. The FiD software is free for academic use and is available for download from www.cs.helsinki.fi/group/sysfys/software/fragid.
Original languageEnglish
Pages (from-to)3043-3052
Number of pages10
JournalRapid Communications in Mass Spectrometry
Volume22
Issue number19
DOIs
Publication statusPublished - 2008
MoE publication typeA1 Journal article-refereed

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Ions
Organic compounds
Metabolism
Yeast
Mass spectrometry
Carbon
Visualization
Molecular weight
Amino Acids
Experiments

Cite this

Heinonen, M., Rantanen, A., Mielikäinen, T., Kokkonen, J., Kiuru, J., Ketola, R. A., & Rousu, J. (2008). FiD: A software for ab initio structural identification of product ions from tandem mass spectrometric data. Rapid Communications in Mass Spectrometry, 22(19), 3043-3052. https://doi.org/10.1002/rcm.3701
Heinonen, Markus ; Rantanen, Ari ; Mielikäinen, Taneli ; Kokkonen, Juha ; Kiuru, Jari ; Ketola, Raimo A. ; Rousu, Juho. / FiD : A software for ab initio structural identification of product ions from tandem mass spectrometric data. In: Rapid Communications in Mass Spectrometry. 2008 ; Vol. 22, No. 19. pp. 3043-3052.
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abstract = "We present FiD (Fragment iDentificator), a software tool for the structural identification of product ions produced with tandem mass spectrometric measurement of low molecular weight organic compounds. Tandem mass spectrometry (MS/MS) has proven to be an indispensable tool in modern, cell‐wide metabolomics and fluxomics studies. In such studies, the structural information of the MSn product ions is usually needed in the downstream analysis of the measurement data. The manual identification of the structures of MSn product ions is, however, a nontrivial task requiring expertise, and calls for computer assistance. Commercial software tools, such as Mass Frontier and ACD/MS Fragmenter, rely on fragmentation rule databases for the identification of MSn product ions. FiD, on the other hand, conducts a combinatorial search over all possible fragmentation paths and outputs a ranked list of alternative structures. This gives the user an advantage in situations where the MS/MS data of compounds with less well‐known fragmentation mechanisms are processed. FiD software implements two fragmentation models, the single‐step model that ignores intermediate fragmentation states and the multi‐step model, which allows for complex fragmentation pathways. The software works for MS/MS data produced both in positive‐ and negative‐ion modes. The software has an easy‐to‐use graphical interface with built‐in visualization capabilities for structures of product ions and fragmentation pathways. In our experiments involving amino acids and sugar‐phosphates, often found, e.g., in the central carbon metabolism of yeasts, FiD software correctly predicted the structures of product ions on average in 85{\%} of the cases. The FiD software is free for academic use and is available for download from www.cs.helsinki.fi/group/sysfys/software/fragid.",
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Heinonen, M, Rantanen, A, Mielikäinen, T, Kokkonen, J, Kiuru, J, Ketola, RA & Rousu, J 2008, 'FiD: A software for ab initio structural identification of product ions from tandem mass spectrometric data', Rapid Communications in Mass Spectrometry, vol. 22, no. 19, pp. 3043-3052. https://doi.org/10.1002/rcm.3701

FiD : A software for ab initio structural identification of product ions from tandem mass spectrometric data. / Heinonen, Markus (Corresponding Author); Rantanen, Ari; Mielikäinen, Taneli; Kokkonen, Juha; Kiuru, Jari; Ketola, Raimo A.; Rousu, Juho.

In: Rapid Communications in Mass Spectrometry, Vol. 22, No. 19, 2008, p. 3043-3052.

Research output: Contribution to journalArticleScientificpeer-review

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T2 - A software for ab initio structural identification of product ions from tandem mass spectrometric data

AU - Heinonen, Markus

AU - Rantanen, Ari

AU - Mielikäinen, Taneli

AU - Kokkonen, Juha

AU - Kiuru, Jari

AU - Ketola, Raimo A.

AU - Rousu, Juho

PY - 2008

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N2 - We present FiD (Fragment iDentificator), a software tool for the structural identification of product ions produced with tandem mass spectrometric measurement of low molecular weight organic compounds. Tandem mass spectrometry (MS/MS) has proven to be an indispensable tool in modern, cell‐wide metabolomics and fluxomics studies. In such studies, the structural information of the MSn product ions is usually needed in the downstream analysis of the measurement data. The manual identification of the structures of MSn product ions is, however, a nontrivial task requiring expertise, and calls for computer assistance. Commercial software tools, such as Mass Frontier and ACD/MS Fragmenter, rely on fragmentation rule databases for the identification of MSn product ions. FiD, on the other hand, conducts a combinatorial search over all possible fragmentation paths and outputs a ranked list of alternative structures. This gives the user an advantage in situations where the MS/MS data of compounds with less well‐known fragmentation mechanisms are processed. FiD software implements two fragmentation models, the single‐step model that ignores intermediate fragmentation states and the multi‐step model, which allows for complex fragmentation pathways. The software works for MS/MS data produced both in positive‐ and negative‐ion modes. The software has an easy‐to‐use graphical interface with built‐in visualization capabilities for structures of product ions and fragmentation pathways. In our experiments involving amino acids and sugar‐phosphates, often found, e.g., in the central carbon metabolism of yeasts, FiD software correctly predicted the structures of product ions on average in 85% of the cases. The FiD software is free for academic use and is available for download from www.cs.helsinki.fi/group/sysfys/software/fragid.

AB - We present FiD (Fragment iDentificator), a software tool for the structural identification of product ions produced with tandem mass spectrometric measurement of low molecular weight organic compounds. Tandem mass spectrometry (MS/MS) has proven to be an indispensable tool in modern, cell‐wide metabolomics and fluxomics studies. In such studies, the structural information of the MSn product ions is usually needed in the downstream analysis of the measurement data. The manual identification of the structures of MSn product ions is, however, a nontrivial task requiring expertise, and calls for computer assistance. Commercial software tools, such as Mass Frontier and ACD/MS Fragmenter, rely on fragmentation rule databases for the identification of MSn product ions. FiD, on the other hand, conducts a combinatorial search over all possible fragmentation paths and outputs a ranked list of alternative structures. This gives the user an advantage in situations where the MS/MS data of compounds with less well‐known fragmentation mechanisms are processed. FiD software implements two fragmentation models, the single‐step model that ignores intermediate fragmentation states and the multi‐step model, which allows for complex fragmentation pathways. The software works for MS/MS data produced both in positive‐ and negative‐ion modes. The software has an easy‐to‐use graphical interface with built‐in visualization capabilities for structures of product ions and fragmentation pathways. In our experiments involving amino acids and sugar‐phosphates, often found, e.g., in the central carbon metabolism of yeasts, FiD software correctly predicted the structures of product ions on average in 85% of the cases. The FiD software is free for academic use and is available for download from www.cs.helsinki.fi/group/sysfys/software/fragid.

U2 - 10.1002/rcm.3701

DO - 10.1002/rcm.3701

M3 - Article

VL - 22

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EP - 3052

JO - Rapid Communications in Mass Spectrometry

JF - Rapid Communications in Mass Spectrometry

SN - 0951-4198

IS - 19

ER -