MetAssign: probabilistic annotation of metabolites from LC-MS data using a Bayesian clustering approach
The use of liquid chromatography coupled to mass spectrometry has enabled the high-throughput profiling of the metabolite composition of biological samples. However, the large amount of data obtained can be difficult to analyse and often requires computational processing to understand which metaboli...
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Veröffentlicht in: | Bioinformatics (Oxford, England) England), 2014-10, Vol.30 (19), p.2764-2771 |
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creator | Daly, Rónán Rogers, Simon Wandy, Joe Jankevics, Andris Burgess, Karl E V Breitling, Rainer |
description | The use of liquid chromatography coupled to mass spectrometry has enabled the high-throughput profiling of the metabolite composition of biological samples. However, the large amount of data obtained can be difficult to analyse and often requires computational processing to understand which metabolites are present in a sample. This article looks at the dual problem of annotating peaks in a sample with a metabolite, together with putatively annotating whether a metabolite is present in the sample. The starting point of the approach is a Bayesian clustering of peaks into groups, each corresponding to putative adducts and isotopes of a single metabolite.
The Bayesian modelling introduced here combines information from the mass-to-charge ratio, retention time and intensity of each peak, together with a model of the inter-peak dependency structure, to increase the accuracy of peak annotation. The results inherently contain a quantitative estimate of confidence in the peak annotations and allow an accurate trade-off between precision and recall. Extensive validation experiments using authentic chemical standards show that this system is able to produce more accurate putative identifications than other state-of-the-art systems, while at the same time giving a probabilistic measure of confidence in the annotations.
The software has been implemented as part of the mzMatch metabolomics analysis pipeline, which is available for download at http://mzmatch.sourceforge.net/. |
doi_str_mv | 10.1093/bioinformatics/btu370 |
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The Bayesian modelling introduced here combines information from the mass-to-charge ratio, retention time and intensity of each peak, together with a model of the inter-peak dependency structure, to increase the accuracy of peak annotation. The results inherently contain a quantitative estimate of confidence in the peak annotations and allow an accurate trade-off between precision and recall. Extensive validation experiments using authentic chemical standards show that this system is able to produce more accurate putative identifications than other state-of-the-art systems, while at the same time giving a probabilistic measure of confidence in the annotations.
The software has been implemented as part of the mzMatch metabolomics analysis pipeline, which is available for download at http://mzmatch.sourceforge.net/.</description><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/btu370</identifier><identifier>PMID: 24916385</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Algorithms ; Bayes Theorem ; Chromatography, Liquid - methods ; Cluster Analysis ; Cysteic Acid - analysis ; Data Interpretation, Statistical ; Mass Spectrometry - methods ; Metabolomics ; Normal Distribution ; Original Papers ; Probability ; Reproducibility of Results ; Software ; Triazoles - analysis</subject><ispartof>Bioinformatics (Oxford, England), 2014-10, Vol.30 (19), p.2764-2771</ispartof><rights>The Author 2014. Published by Oxford University Press.</rights><rights>The Author 2014. Published by Oxford University Press. 2014</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c411t-ddcdfaa7be4eaa3ee68425fc1d6a8d7b4f1124746b9474107e11447ebe1c258f3</citedby><cites>FETCH-LOGICAL-c411t-ddcdfaa7be4eaa3ee68425fc1d6a8d7b4f1124746b9474107e11447ebe1c258f3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4173012/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4173012/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24916385$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Daly, Rónán</creatorcontrib><creatorcontrib>Rogers, Simon</creatorcontrib><creatorcontrib>Wandy, Joe</creatorcontrib><creatorcontrib>Jankevics, Andris</creatorcontrib><creatorcontrib>Burgess, Karl E V</creatorcontrib><creatorcontrib>Breitling, Rainer</creatorcontrib><title>MetAssign: probabilistic annotation of metabolites from LC-MS data using a Bayesian clustering approach</title><title>Bioinformatics (Oxford, England)</title><addtitle>Bioinformatics</addtitle><description>The use of liquid chromatography coupled to mass spectrometry has enabled the high-throughput profiling of the metabolite composition of biological samples. However, the large amount of data obtained can be difficult to analyse and often requires computational processing to understand which metabolites are present in a sample. This article looks at the dual problem of annotating peaks in a sample with a metabolite, together with putatively annotating whether a metabolite is present in the sample. The starting point of the approach is a Bayesian clustering of peaks into groups, each corresponding to putative adducts and isotopes of a single metabolite.
The Bayesian modelling introduced here combines information from the mass-to-charge ratio, retention time and intensity of each peak, together with a model of the inter-peak dependency structure, to increase the accuracy of peak annotation. The results inherently contain a quantitative estimate of confidence in the peak annotations and allow an accurate trade-off between precision and recall. Extensive validation experiments using authentic chemical standards show that this system is able to produce more accurate putative identifications than other state-of-the-art systems, while at the same time giving a probabilistic measure of confidence in the annotations.
The software has been implemented as part of the mzMatch metabolomics analysis pipeline, which is available for download at http://mzmatch.sourceforge.net/.</description><subject>Algorithms</subject><subject>Bayes Theorem</subject><subject>Chromatography, Liquid - methods</subject><subject>Cluster Analysis</subject><subject>Cysteic Acid - analysis</subject><subject>Data Interpretation, Statistical</subject><subject>Mass Spectrometry - methods</subject><subject>Metabolomics</subject><subject>Normal Distribution</subject><subject>Original Papers</subject><subject>Probability</subject><subject>Reproducibility of Results</subject><subject>Software</subject><subject>Triazoles - analysis</subject><issn>1367-4803</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpVkUtvFDEMx6MK1JbCR6DKkcvQeJJ5bA-V2lV5SFtxAM6Rk3G2QTPJNslU6rdnYMuKXmzLj58t_xl7D-IjiJW8MD764GKasHibL0yZZSeO2CnItqtUD_DqEAt5wt7k_EsI0YimPWYntVpBK_vmlG3vqFzn7Lfhku9SNGj86POC5BhCLAs8Bh4dn6igiaMvlLlLceKbdXX3nQ9YkM_Zhy1HfoNPlD0Gbsc5F0p_s7uFivb-LXvtcMz07tmfsZ-fbn-sv1Sbb5-_rq83lVUApRoGOzjEzpAiREnU9qpunIWhxX7ojHIAtepUa1aLBdERgFIdGQJbN72TZ-xqz93NZqLBUigJR71LfsL0pCN6_bIS_L3exketoJMC6gXw4RmQ4sNMuejJZ0vjiIHinDU0bQsglqcurc2-1aaYcyJ3WANC_xFJvxRJ70Va5s7_v_Ew9U8V-RuIjZbb</recordid><startdate>20141001</startdate><enddate>20141001</enddate><creator>Daly, Rónán</creator><creator>Rogers, Simon</creator><creator>Wandy, Joe</creator><creator>Jankevics, Andris</creator><creator>Burgess, Karl E V</creator><creator>Breitling, Rainer</creator><general>Oxford University Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20141001</creationdate><title>MetAssign: probabilistic annotation of metabolites from LC-MS data using a Bayesian clustering approach</title><author>Daly, Rónán ; Rogers, Simon ; Wandy, Joe ; Jankevics, Andris ; Burgess, Karl E V ; Breitling, Rainer</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c411t-ddcdfaa7be4eaa3ee68425fc1d6a8d7b4f1124746b9474107e11447ebe1c258f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Algorithms</topic><topic>Bayes Theorem</topic><topic>Chromatography, Liquid - methods</topic><topic>Cluster Analysis</topic><topic>Cysteic Acid - analysis</topic><topic>Data Interpretation, Statistical</topic><topic>Mass Spectrometry - methods</topic><topic>Metabolomics</topic><topic>Normal Distribution</topic><topic>Original Papers</topic><topic>Probability</topic><topic>Reproducibility of Results</topic><topic>Software</topic><topic>Triazoles - analysis</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Daly, Rónán</creatorcontrib><creatorcontrib>Rogers, Simon</creatorcontrib><creatorcontrib>Wandy, Joe</creatorcontrib><creatorcontrib>Jankevics, Andris</creatorcontrib><creatorcontrib>Burgess, Karl E V</creatorcontrib><creatorcontrib>Breitling, Rainer</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Bioinformatics (Oxford, England)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Daly, Rónán</au><au>Rogers, Simon</au><au>Wandy, Joe</au><au>Jankevics, Andris</au><au>Burgess, Karl E V</au><au>Breitling, Rainer</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>MetAssign: probabilistic annotation of metabolites from LC-MS data using a Bayesian clustering approach</atitle><jtitle>Bioinformatics (Oxford, England)</jtitle><addtitle>Bioinformatics</addtitle><date>2014-10-01</date><risdate>2014</risdate><volume>30</volume><issue>19</issue><spage>2764</spage><epage>2771</epage><pages>2764-2771</pages><issn>1367-4803</issn><eissn>1367-4811</eissn><abstract>The use of liquid chromatography coupled to mass spectrometry has enabled the high-throughput profiling of the metabolite composition of biological samples. However, the large amount of data obtained can be difficult to analyse and often requires computational processing to understand which metabolites are present in a sample. This article looks at the dual problem of annotating peaks in a sample with a metabolite, together with putatively annotating whether a metabolite is present in the sample. The starting point of the approach is a Bayesian clustering of peaks into groups, each corresponding to putative adducts and isotopes of a single metabolite.
The Bayesian modelling introduced here combines information from the mass-to-charge ratio, retention time and intensity of each peak, together with a model of the inter-peak dependency structure, to increase the accuracy of peak annotation. The results inherently contain a quantitative estimate of confidence in the peak annotations and allow an accurate trade-off between precision and recall. Extensive validation experiments using authentic chemical standards show that this system is able to produce more accurate putative identifications than other state-of-the-art systems, while at the same time giving a probabilistic measure of confidence in the annotations.
The software has been implemented as part of the mzMatch metabolomics analysis pipeline, which is available for download at http://mzmatch.sourceforge.net/.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>24916385</pmid><doi>10.1093/bioinformatics/btu370</doi><tpages>8</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Algorithms Bayes Theorem Chromatography, Liquid - methods Cluster Analysis Cysteic Acid - analysis Data Interpretation, Statistical Mass Spectrometry - methods Metabolomics Normal Distribution Original Papers Probability Reproducibility of Results Software Triazoles - analysis |
title | MetAssign: probabilistic annotation of metabolites from LC-MS data using a Bayesian clustering approach |
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