Mass spectra-based framework for automated structural elucidation of metabolome data to explore phytochemical diversity
A novel framework for automated elucidation of metabolite structures in liquid chromatography-mass spectrometer (LC-MS) metabolome data was constructed by integrating databases. High-resolution tandem mass spectra data automatically acquired from each metabolite signal were used for database searche...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2011-08-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2011.00040/full |
| _version_ | 1819053792039010304 |
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| author | Fumio eMatsuda Fumio eMatsuda Ryo eNakabayashi Yuji eSawada Yuji eSawada Makoto eSuzuki Masami Yokota Hirai Masami Yokota Hirai Shigehiko eKanaya Kazuki eSaito Kazuki eSaito |
| author_facet | Fumio eMatsuda Fumio eMatsuda Ryo eNakabayashi Yuji eSawada Yuji eSawada Makoto eSuzuki Masami Yokota Hirai Masami Yokota Hirai Shigehiko eKanaya Kazuki eSaito Kazuki eSaito |
| author_sort | Fumio eMatsuda |
| collection | DOAJ |
| description | A novel framework for automated elucidation of metabolite structures in liquid chromatography-mass spectrometer (LC-MS) metabolome data was constructed by integrating databases. High-resolution tandem mass spectra data automatically acquired from each metabolite signal were used for database searches. Three distinct databases, KNApSAcK, ReSpect, and the PRIMe standard compound database, were employed for the structural elucidation. The outputs were retrieved using the CAS metabolite identifier for identification and putative annotation. A simple metabolite ontology system was also introduced to attain putative characterization of the metabolite signals. The automated method was applied for the metabolome data sets obtained from the rosette leaves of 20 Arabidopsis accessions. Phenotypic variations in novel Arabidopsis metabolites among these accessions could be investigated using this method. |
| first_indexed | 2024-12-21T12:41:21Z |
| format | Article |
| id | doaj.art-06beb025cb074ff6a00cddac9c6be074 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-21T12:41:21Z |
| publishDate | 2011-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-06beb025cb074ff6a00cddac9c6be0742022-12-21T19:03:46ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2011-08-01210.3389/fpls.2011.0004011423Mass spectra-based framework for automated structural elucidation of metabolome data to explore phytochemical diversityFumio eMatsuda0Fumio eMatsuda1Ryo eNakabayashi2Yuji eSawada3Yuji eSawada4Makoto eSuzuki5Masami Yokota Hirai6Masami Yokota Hirai7Shigehiko eKanaya8Kazuki eSaito9Kazuki eSaito10Kobe UniversityRIKEN Plant Science CenterRIKEN Plant Science CenterRIKEN Plant Science CenterJapan Science and Technology AgencyRIKEN Plant Science CenterRIKEN Plant Science CenterJapan Science and Technology AgencyNara Institute of Science and TechnologyRIKEN Plant Science CenterChiba UniversityA novel framework for automated elucidation of metabolite structures in liquid chromatography-mass spectrometer (LC-MS) metabolome data was constructed by integrating databases. High-resolution tandem mass spectra data automatically acquired from each metabolite signal were used for database searches. Three distinct databases, KNApSAcK, ReSpect, and the PRIMe standard compound database, were employed for the structural elucidation. The outputs were retrieved using the CAS metabolite identifier for identification and putative annotation. A simple metabolite ontology system was also introduced to attain putative characterization of the metabolite signals. The automated method was applied for the metabolome data sets obtained from the rosette leaves of 20 Arabidopsis accessions. Phenotypic variations in novel Arabidopsis metabolites among these accessions could be investigated using this method.http://journal.frontiersin.org/Journal/10.3389/fpls.2011.00040/fulldatabase searchingliquid chromatography-mass spectrometrymetabolite ontologymetabolome analysisnatural variations in secondary metabolitestructural elucidation |
| spellingShingle | Fumio eMatsuda Fumio eMatsuda Ryo eNakabayashi Yuji eSawada Yuji eSawada Makoto eSuzuki Masami Yokota Hirai Masami Yokota Hirai Shigehiko eKanaya Kazuki eSaito Kazuki eSaito Mass spectra-based framework for automated structural elucidation of metabolome data to explore phytochemical diversity Frontiers in Plant Science database searching liquid chromatography-mass spectrometry metabolite ontology metabolome analysis natural variations in secondary metabolite structural elucidation |
| title | Mass spectra-based framework for automated structural elucidation of metabolome data to explore phytochemical diversity |
| title_full | Mass spectra-based framework for automated structural elucidation of metabolome data to explore phytochemical diversity |
| title_fullStr | Mass spectra-based framework for automated structural elucidation of metabolome data to explore phytochemical diversity |
| title_full_unstemmed | Mass spectra-based framework for automated structural elucidation of metabolome data to explore phytochemical diversity |
| title_short | Mass spectra-based framework for automated structural elucidation of metabolome data to explore phytochemical diversity |
| title_sort | mass spectra based framework for automated structural elucidation of metabolome data to explore phytochemical diversity |
| topic | database searching liquid chromatography-mass spectrometry metabolite ontology metabolome analysis natural variations in secondary metabolite structural elucidation |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2011.00040/full |
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