The importance of mass spectrometric dereplication in fungal secondary metabolite analysis
Having entered the Genomic Era, it is now evident that the biosynthetic potential of filamentous fungi is much larger than was thought even a decade ago. Fungi harbor many cryptic gene clusters encoding for the biosynthesis of polyketides, non-ribosomal peptides, and terpenoids – which can all under...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2015-02-01
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| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00071/full |
| _version_ | 1828752385853358080 |
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| author | Kristian Fog Nielsen Thomas Ostenfeld Larsen |
| author_facet | Kristian Fog Nielsen Thomas Ostenfeld Larsen |
| author_sort | Kristian Fog Nielsen |
| collection | DOAJ |
| description | Having entered the Genomic Era, it is now evident that the biosynthetic potential of filamentous fungi is much larger than was thought even a decade ago. Fungi harbor many cryptic gene clusters encoding for the biosynthesis of polyketides, non-ribosomal peptides, and terpenoids – which can all undergo extensive modifications by tailoring enzymes – thus potentially providing a large array of products from a single pathway. Elucidating the full chemical profile of a fungal species is a challenging exercise, even with elemental composition provided by high-resolution mass spectrometry (HRMS) used in combination with chemical databases (e.g. Antibase) to dereplicate known compounds. This has led to a continuous effort to improve chromatographic separation in conjunction with improvement in HRMS detection. Major improvements have also occurred with 2D chromatography, ion-mobility, MS/MS and MS3, stable isotope labeling feeding experiments, classic UV/Vis, and especially automated data-mining and metabolomics software approaches as the sheer amount of data generated is now the major challenge. This review will focus on the development and implementation of dereplication strategies and will highlight the importance of each stage of the process from sample preparation to chromatographic separation and finally towards both manual and more targeted methods for automated dereplication of fungal natural products using state-of-the art MS instrumentation. |
| first_indexed | 2024-12-10T21:09:01Z |
| format | Article |
| id | doaj.art-60b6af3601f94f2981567c645920b4b5 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-10T21:09:01Z |
| publishDate | 2015-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-60b6af3601f94f2981567c645920b4b52022-12-22T01:33:33ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2015-02-01610.3389/fmicb.2015.00071128201The importance of mass spectrometric dereplication in fungal secondary metabolite analysisKristian Fog Nielsen0Thomas Ostenfeld Larsen1Technical University of DenmarkTechnical University of DenmarkHaving entered the Genomic Era, it is now evident that the biosynthetic potential of filamentous fungi is much larger than was thought even a decade ago. Fungi harbor many cryptic gene clusters encoding for the biosynthesis of polyketides, non-ribosomal peptides, and terpenoids – which can all undergo extensive modifications by tailoring enzymes – thus potentially providing a large array of products from a single pathway. Elucidating the full chemical profile of a fungal species is a challenging exercise, even with elemental composition provided by high-resolution mass spectrometry (HRMS) used in combination with chemical databases (e.g. Antibase) to dereplicate known compounds. This has led to a continuous effort to improve chromatographic separation in conjunction with improvement in HRMS detection. Major improvements have also occurred with 2D chromatography, ion-mobility, MS/MS and MS3, stable isotope labeling feeding experiments, classic UV/Vis, and especially automated data-mining and metabolomics software approaches as the sheer amount of data generated is now the major challenge. This review will focus on the development and implementation of dereplication strategies and will highlight the importance of each stage of the process from sample preparation to chromatographic separation and finally towards both manual and more targeted methods for automated dereplication of fungal natural products using state-of-the art MS instrumentation.http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00071/fullMass SpectrometryMetabolomicsLiquid ChromatographyDiode array detectiondereplication. |
| spellingShingle | Kristian Fog Nielsen Thomas Ostenfeld Larsen The importance of mass spectrometric dereplication in fungal secondary metabolite analysis Frontiers in Microbiology Mass Spectrometry Metabolomics Liquid Chromatography Diode array detection dereplication. |
| title | The importance of mass spectrometric dereplication in fungal secondary metabolite analysis |
| title_full | The importance of mass spectrometric dereplication in fungal secondary metabolite analysis |
| title_fullStr | The importance of mass spectrometric dereplication in fungal secondary metabolite analysis |
| title_full_unstemmed | The importance of mass spectrometric dereplication in fungal secondary metabolite analysis |
| title_short | The importance of mass spectrometric dereplication in fungal secondary metabolite analysis |
| title_sort | importance of mass spectrometric dereplication in fungal secondary metabolite analysis |
| topic | Mass Spectrometry Metabolomics Liquid Chromatography Diode array detection dereplication. |
| url | http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00071/full |
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