Assessment of metabolome annotation quality: a method for evaluating the false discovery rate of elemental composition searches.
BACKGROUND: In metabolomics researches using mass spectrometry (MS), systematic searching of high-resolution mass data against compound databases is often the first step of metabolite annotation to determine elemental compositions possessing similar theoretical mass numbers. However, incorrect hits...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2009-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC2761541?pdf=render |
| _version_ | 1819265230567374848 |
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| author | Fumio Matsuda Yoko Shinbo Akira Oikawa Masami Yokota Hirai Oliver Fiehn Shigehiko Kanaya Kazuki Saito |
| author_facet | Fumio Matsuda Yoko Shinbo Akira Oikawa Masami Yokota Hirai Oliver Fiehn Shigehiko Kanaya Kazuki Saito |
| author_sort | Fumio Matsuda |
| collection | DOAJ |
| description | BACKGROUND: In metabolomics researches using mass spectrometry (MS), systematic searching of high-resolution mass data against compound databases is often the first step of metabolite annotation to determine elemental compositions possessing similar theoretical mass numbers. However, incorrect hits derived from errors in mass analyses will be included in the results of elemental composition searches. To assess the quality of peak annotation information, a novel methodology for false discovery rates (FDR) evaluation is presented in this study. Based on the FDR analyses, several aspects of an elemental composition search, including setting a threshold, estimating FDR, and the types of elemental composition databases most reliable for searching are discussed. METHODOLOGY/PRINCIPAL FINDINGS: The FDR can be determined from one measured value (i.e., the hit rate for search queries) and four parameters determined by Monte Carlo simulation. The results indicate that relatively high FDR values (30-50%) were obtained when searching time-of-flight (TOF)/MS data using the KNApSAcK and KEGG databases. In addition, searches against large all-in-one databases (e.g., PubChem) always produced unacceptable results (FDR >70%). The estimated FDRs suggest that the quality of search results can be improved not only by performing more accurate mass analysis but also by modifying the properties of the compound database. A theoretical analysis indicates that FDR could be improved by using compound database with smaller but higher completeness entries. CONCLUSIONS/SIGNIFICANCE: High accuracy mass analysis, such as Fourier transform (FT)-MS, is needed for reliable annotation (FDR <10%). In addition, a small, customized compound database is preferable for high-quality annotation of metabolome data. |
| first_indexed | 2024-12-23T20:42:05Z |
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| id | doaj.art-2fa835191288442db982270f41be510d |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-23T20:42:05Z |
| publishDate | 2009-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-2fa835191288442db982270f41be510d2022-12-21T17:31:53ZengPublic Library of Science (PLoS)PLoS ONE1932-62032009-01-01410e749010.1371/journal.pone.0007490Assessment of metabolome annotation quality: a method for evaluating the false discovery rate of elemental composition searches.Fumio MatsudaYoko ShinboAkira OikawaMasami Yokota HiraiOliver FiehnShigehiko KanayaKazuki SaitoBACKGROUND: In metabolomics researches using mass spectrometry (MS), systematic searching of high-resolution mass data against compound databases is often the first step of metabolite annotation to determine elemental compositions possessing similar theoretical mass numbers. However, incorrect hits derived from errors in mass analyses will be included in the results of elemental composition searches. To assess the quality of peak annotation information, a novel methodology for false discovery rates (FDR) evaluation is presented in this study. Based on the FDR analyses, several aspects of an elemental composition search, including setting a threshold, estimating FDR, and the types of elemental composition databases most reliable for searching are discussed. METHODOLOGY/PRINCIPAL FINDINGS: The FDR can be determined from one measured value (i.e., the hit rate for search queries) and four parameters determined by Monte Carlo simulation. The results indicate that relatively high FDR values (30-50%) were obtained when searching time-of-flight (TOF)/MS data using the KNApSAcK and KEGG databases. In addition, searches against large all-in-one databases (e.g., PubChem) always produced unacceptable results (FDR >70%). The estimated FDRs suggest that the quality of search results can be improved not only by performing more accurate mass analysis but also by modifying the properties of the compound database. A theoretical analysis indicates that FDR could be improved by using compound database with smaller but higher completeness entries. CONCLUSIONS/SIGNIFICANCE: High accuracy mass analysis, such as Fourier transform (FT)-MS, is needed for reliable annotation (FDR <10%). In addition, a small, customized compound database is preferable for high-quality annotation of metabolome data.http://europepmc.org/articles/PMC2761541?pdf=render |
| spellingShingle | Fumio Matsuda Yoko Shinbo Akira Oikawa Masami Yokota Hirai Oliver Fiehn Shigehiko Kanaya Kazuki Saito Assessment of metabolome annotation quality: a method for evaluating the false discovery rate of elemental composition searches. PLoS ONE |
| title | Assessment of metabolome annotation quality: a method for evaluating the false discovery rate of elemental composition searches. |
| title_full | Assessment of metabolome annotation quality: a method for evaluating the false discovery rate of elemental composition searches. |
| title_fullStr | Assessment of metabolome annotation quality: a method for evaluating the false discovery rate of elemental composition searches. |
| title_full_unstemmed | Assessment of metabolome annotation quality: a method for evaluating the false discovery rate of elemental composition searches. |
| title_short | Assessment of metabolome annotation quality: a method for evaluating the false discovery rate of elemental composition searches. |
| title_sort | assessment of metabolome annotation quality a method for evaluating the false discovery rate of elemental composition searches |
| url | http://europepmc.org/articles/PMC2761541?pdf=render |
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