Protocol for community‐created public MS/MS reference spectra within the Global Natural Products Social Molecular Networking infrastructure
Rationale A major hurdle in identifying chemicals in mass spectrometry experiments is the availability of tandem mass spectrometry (MS/MS) reference spectra in public databases. Currently, scientists purchase databases or use public databases such as Global Natural Products Social Molecular Networki...
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| Veröffentlicht in: | Rapid communications in mass spectrometry 2020-05, Vol.34 (10), p.e8725-n/a |
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| creator | Vargas, Fernando Weldon, Kelly C. Sikora, Nicole Wang, Mingxun Zhang, Zheng Gentry, Emily C. Panitchpakdi, Morgan W. Caraballo‐Rodríguez, Andrés Mauricio Dorrestein, Pieter C. Jarmusch, Alan K. |
| description | Rationale
A major hurdle in identifying chemicals in mass spectrometry experiments is the availability of tandem mass spectrometry (MS/MS) reference spectra in public databases. Currently, scientists purchase databases or use public databases such as Global Natural Products Social Molecular Networking (GNPS). The MSMS‐Chooser workflow is an open‐source protocol for the creation of MS/MS reference spectra directly in the GNPS infrastructure.
Methods
An MSMS‐Chooser Sample Template is provided and completed manually. The MSMS‐Chooser Submission File and Sequence Table for data acquisition were programmatically generated. Standards from the Mass Spectrometry Metabolite Library (MSMLS) suspended in a methanol–water (1:1) solution were analyzed. Flow injection on an LC/MS/MS system was used to generate negative and positive mode data using data‐dependent acquisition. The MS/MS spectra and Submission File were uploaded to MSMS‐Chooser workflow in GNPS for automatic selection of MS/MS spectra.
Results
Data acquisition and processing required ~2 h and ~2 min, respectively, per 96‐well plate using MSMS‐Chooser. Analysis of the MSMLS, over 600 small molecules, using MSMS‐Chooser added 889 spectra (including multiple adducts) to the public library in GNPS. Manual validation of one plate indicated accurate selection of MS/MS scans (true positive rate of 0.96 and a true negative rate of 0.99). The MSMS‐Chooser output includes a table formatted for inclusion in the GNPS library as well as the ability to directly launch searches via MASST.
Conclusions
MSMS‐Chooser enables rapid data acquisition, data analysis (selection of MS/MS spectra), and a formatted table for inspection and upload to GNPS. Open file‐format data (.mzML or.mzXML) from most mass spectrometry platforms containing MS/MS spectra can be processed using MSMS‐Chooser. MSMS‐Chooser democratizes the creation of MS/MS reference spectra in GNPS which will improve annotation and strengthen the tools which use the annotation information. |
| doi_str_mv | 10.1002/rcm.8725 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_2338068931</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2393315987</sourcerecordid><originalsourceid>FETCH-LOGICAL-c4155-56b548011bbd7b60d744b0f23fd71fee8e69d371458165c014c5980d725c60d63</originalsourceid><addsrcrecordid>eNp1kdFqFDEUhkNR2rUW-gQl4I030yaTyWTmUpZahW4VV6-HTOaMTZuZrCcJy975AoLP6JOY2tqC4NXPgY-Pc85PyDFnp5yx8gzNdNqoUu6RBWetKlgp-DOyYK3kRcXb5oC8COGGMc5lyfbJgeCtYEqqBfnxEX30xjs6eqTGT1Oabdz9-v7TIOgIA92k3llDV-uz1ZoijIAwG6BhAyaiplsbr-1M4zXQC-d77eiVjglzZvOQTAx07Y3N88o7MMlppFcQtx5v7fyV2nlEHSJmMCG8JM9H7QIcPeQh-fL2_PPyXXH54eL98s1lYSouZSHrXlZNvqbvB9XXbFBV1bOxFOOg-AjQQN0OQvFKNryWhvHKyLbJWClNpmtxSF7fezfovyUIsZtsMOCcnsGn0JVCNKxuWsEz-uof9MYnnPN2mWqF4NmsnoQGfQj5S90G7aRx13HW3VXU5Yq6u4oyevIgTP0EwyP4t5MMFPfA1jrY_VfUfVqu_gh_A9OLnJE</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2393315987</pqid></control><display><type>article</type><title>Protocol for community‐created public MS/MS reference spectra within the Global Natural Products Social Molecular Networking infrastructure</title><source>Wiley Online Library Journals Frontfile Complete</source><creator>Vargas, Fernando ; Weldon, Kelly C. ; Sikora, Nicole ; Wang, Mingxun ; Zhang, Zheng ; Gentry, Emily C. ; Panitchpakdi, Morgan W. ; Caraballo‐Rodríguez, Andrés Mauricio ; Dorrestein, Pieter C. ; Jarmusch, Alan K.</creator><creatorcontrib>Vargas, Fernando ; Weldon, Kelly C. ; Sikora, Nicole ; Wang, Mingxun ; Zhang, Zheng ; Gentry, Emily C. ; Panitchpakdi, Morgan W. ; Caraballo‐Rodríguez, Andrés Mauricio ; Dorrestein, Pieter C. ; Jarmusch, Alan K.</creatorcontrib><description>Rationale
A major hurdle in identifying chemicals in mass spectrometry experiments is the availability of tandem mass spectrometry (MS/MS) reference spectra in public databases. Currently, scientists purchase databases or use public databases such as Global Natural Products Social Molecular Networking (GNPS). The MSMS‐Chooser workflow is an open‐source protocol for the creation of MS/MS reference spectra directly in the GNPS infrastructure.
Methods
An MSMS‐Chooser Sample Template is provided and completed manually. The MSMS‐Chooser Submission File and Sequence Table for data acquisition were programmatically generated. Standards from the Mass Spectrometry Metabolite Library (MSMLS) suspended in a methanol–water (1:1) solution were analyzed. Flow injection on an LC/MS/MS system was used to generate negative and positive mode data using data‐dependent acquisition. The MS/MS spectra and Submission File were uploaded to MSMS‐Chooser workflow in GNPS for automatic selection of MS/MS spectra.
Results
Data acquisition and processing required ~2 h and ~2 min, respectively, per 96‐well plate using MSMS‐Chooser. Analysis of the MSMLS, over 600 small molecules, using MSMS‐Chooser added 889 spectra (including multiple adducts) to the public library in GNPS. Manual validation of one plate indicated accurate selection of MS/MS scans (true positive rate of 0.96 and a true negative rate of 0.99). The MSMS‐Chooser output includes a table formatted for inclusion in the GNPS library as well as the ability to directly launch searches via MASST.
Conclusions
MSMS‐Chooser enables rapid data acquisition, data analysis (selection of MS/MS spectra), and a formatted table for inspection and upload to GNPS. Open file‐format data (.mzML or.mzXML) from most mass spectrometry platforms containing MS/MS spectra can be processed using MSMS‐Chooser. MSMS‐Chooser democratizes the creation of MS/MS reference spectra in GNPS which will improve annotation and strengthen the tools which use the annotation information.</description><identifier>ISSN: 0951-4198</identifier><identifier>EISSN: 1097-0231</identifier><identifier>DOI: 10.1002/rcm.8725</identifier><identifier>PMID: 31930757</identifier><language>eng</language><publisher>England: Wiley Subscription Services, Inc</publisher><subject>Adducts ; Annotations ; Data analysis ; Infrastructure ; Inspection ; Libraries ; Mass spectrometry ; Metabolites ; Natural products ; Scientific imaging ; Spectra ; Spectroscopy ; Workflow</subject><ispartof>Rapid communications in mass spectrometry, 2020-05, Vol.34 (10), p.e8725-n/a</ispartof><rights>2020 John Wiley & Sons, Ltd.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4155-56b548011bbd7b60d744b0f23fd71fee8e69d371458165c014c5980d725c60d63</citedby><cites>FETCH-LOGICAL-c4155-56b548011bbd7b60d744b0f23fd71fee8e69d371458165c014c5980d725c60d63</cites><orcidid>0000-0003-1064-8153 ; 0000-0002-0016-8132 ; 0000-0001-5499-2728 ; 0000-0002-3003-1030 ; 0000-0001-5847-2439 ; 0000-0001-7647-6097 ; 0000-0002-2228-6308</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Frcm.8725$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Frcm.8725$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31930757$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Vargas, Fernando</creatorcontrib><creatorcontrib>Weldon, Kelly C.</creatorcontrib><creatorcontrib>Sikora, Nicole</creatorcontrib><creatorcontrib>Wang, Mingxun</creatorcontrib><creatorcontrib>Zhang, Zheng</creatorcontrib><creatorcontrib>Gentry, Emily C.</creatorcontrib><creatorcontrib>Panitchpakdi, Morgan W.</creatorcontrib><creatorcontrib>Caraballo‐Rodríguez, Andrés Mauricio</creatorcontrib><creatorcontrib>Dorrestein, Pieter C.</creatorcontrib><creatorcontrib>Jarmusch, Alan K.</creatorcontrib><title>Protocol for community‐created public MS/MS reference spectra within the Global Natural Products Social Molecular Networking infrastructure</title><title>Rapid communications in mass spectrometry</title><addtitle>Rapid Commun Mass Spectrom</addtitle><description>Rationale
A major hurdle in identifying chemicals in mass spectrometry experiments is the availability of tandem mass spectrometry (MS/MS) reference spectra in public databases. Currently, scientists purchase databases or use public databases such as Global Natural Products Social Molecular Networking (GNPS). The MSMS‐Chooser workflow is an open‐source protocol for the creation of MS/MS reference spectra directly in the GNPS infrastructure.
Methods
An MSMS‐Chooser Sample Template is provided and completed manually. The MSMS‐Chooser Submission File and Sequence Table for data acquisition were programmatically generated. Standards from the Mass Spectrometry Metabolite Library (MSMLS) suspended in a methanol–water (1:1) solution were analyzed. Flow injection on an LC/MS/MS system was used to generate negative and positive mode data using data‐dependent acquisition. The MS/MS spectra and Submission File were uploaded to MSMS‐Chooser workflow in GNPS for automatic selection of MS/MS spectra.
Results
Data acquisition and processing required ~2 h and ~2 min, respectively, per 96‐well plate using MSMS‐Chooser. Analysis of the MSMLS, over 600 small molecules, using MSMS‐Chooser added 889 spectra (including multiple adducts) to the public library in GNPS. Manual validation of one plate indicated accurate selection of MS/MS scans (true positive rate of 0.96 and a true negative rate of 0.99). The MSMS‐Chooser output includes a table formatted for inclusion in the GNPS library as well as the ability to directly launch searches via MASST.
Conclusions
MSMS‐Chooser enables rapid data acquisition, data analysis (selection of MS/MS spectra), and a formatted table for inspection and upload to GNPS. Open file‐format data (.mzML or.mzXML) from most mass spectrometry platforms containing MS/MS spectra can be processed using MSMS‐Chooser. MSMS‐Chooser democratizes the creation of MS/MS reference spectra in GNPS which will improve annotation and strengthen the tools which use the annotation information.</description><subject>Adducts</subject><subject>Annotations</subject><subject>Data analysis</subject><subject>Infrastructure</subject><subject>Inspection</subject><subject>Libraries</subject><subject>Mass spectrometry</subject><subject>Metabolites</subject><subject>Natural products</subject><subject>Scientific imaging</subject><subject>Spectra</subject><subject>Spectroscopy</subject><subject>Workflow</subject><issn>0951-4198</issn><issn>1097-0231</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><recordid>eNp1kdFqFDEUhkNR2rUW-gQl4I030yaTyWTmUpZahW4VV6-HTOaMTZuZrCcJy975AoLP6JOY2tqC4NXPgY-Pc85PyDFnp5yx8gzNdNqoUu6RBWetKlgp-DOyYK3kRcXb5oC8COGGMc5lyfbJgeCtYEqqBfnxEX30xjs6eqTGT1Oabdz9-v7TIOgIA92k3llDV-uz1ZoijIAwG6BhAyaiplsbr-1M4zXQC-d77eiVjglzZvOQTAx07Y3N88o7MMlppFcQtx5v7fyV2nlEHSJmMCG8JM9H7QIcPeQh-fL2_PPyXXH54eL98s1lYSouZSHrXlZNvqbvB9XXbFBV1bOxFOOg-AjQQN0OQvFKNryWhvHKyLbJWClNpmtxSF7fezfovyUIsZtsMOCcnsGn0JVCNKxuWsEz-uof9MYnnPN2mWqF4NmsnoQGfQj5S90G7aRx13HW3VXU5Yq6u4oyevIgTP0EwyP4t5MMFPfA1jrY_VfUfVqu_gh_A9OLnJE</recordid><startdate>20200530</startdate><enddate>20200530</enddate><creator>Vargas, Fernando</creator><creator>Weldon, Kelly C.</creator><creator>Sikora, Nicole</creator><creator>Wang, Mingxun</creator><creator>Zhang, Zheng</creator><creator>Gentry, Emily C.</creator><creator>Panitchpakdi, Morgan W.</creator><creator>Caraballo‐Rodríguez, Andrés Mauricio</creator><creator>Dorrestein, Pieter C.</creator><creator>Jarmusch, Alan K.</creator><general>Wiley Subscription Services, Inc</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7SR</scope><scope>7U5</scope><scope>8BQ</scope><scope>8FD</scope><scope>JG9</scope><scope>JQ2</scope><scope>L7M</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0003-1064-8153</orcidid><orcidid>https://orcid.org/0000-0002-0016-8132</orcidid><orcidid>https://orcid.org/0000-0001-5499-2728</orcidid><orcidid>https://orcid.org/0000-0002-3003-1030</orcidid><orcidid>https://orcid.org/0000-0001-5847-2439</orcidid><orcidid>https://orcid.org/0000-0001-7647-6097</orcidid><orcidid>https://orcid.org/0000-0002-2228-6308</orcidid></search><sort><creationdate>20200530</creationdate><title>Protocol for community‐created public MS/MS reference spectra within the Global Natural Products Social Molecular Networking infrastructure</title><author>Vargas, Fernando ; Weldon, Kelly C. ; Sikora, Nicole ; Wang, Mingxun ; Zhang, Zheng ; Gentry, Emily C. ; Panitchpakdi, Morgan W. ; Caraballo‐Rodríguez, Andrés Mauricio ; Dorrestein, Pieter C. ; Jarmusch, Alan K.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4155-56b548011bbd7b60d744b0f23fd71fee8e69d371458165c014c5980d725c60d63</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Adducts</topic><topic>Annotations</topic><topic>Data analysis</topic><topic>Infrastructure</topic><topic>Inspection</topic><topic>Libraries</topic><topic>Mass spectrometry</topic><topic>Metabolites</topic><topic>Natural products</topic><topic>Scientific imaging</topic><topic>Spectra</topic><topic>Spectroscopy</topic><topic>Workflow</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Vargas, Fernando</creatorcontrib><creatorcontrib>Weldon, Kelly C.</creatorcontrib><creatorcontrib>Sikora, Nicole</creatorcontrib><creatorcontrib>Wang, Mingxun</creatorcontrib><creatorcontrib>Zhang, Zheng</creatorcontrib><creatorcontrib>Gentry, Emily C.</creatorcontrib><creatorcontrib>Panitchpakdi, Morgan W.</creatorcontrib><creatorcontrib>Caraballo‐Rodríguez, Andrés Mauricio</creatorcontrib><creatorcontrib>Dorrestein, Pieter C.</creatorcontrib><creatorcontrib>Jarmusch, Alan K.</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>Engineered Materials Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>Materials Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>MEDLINE - Academic</collection><jtitle>Rapid communications in mass spectrometry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Vargas, Fernando</au><au>Weldon, Kelly C.</au><au>Sikora, Nicole</au><au>Wang, Mingxun</au><au>Zhang, Zheng</au><au>Gentry, Emily C.</au><au>Panitchpakdi, Morgan W.</au><au>Caraballo‐Rodríguez, Andrés Mauricio</au><au>Dorrestein, Pieter C.</au><au>Jarmusch, Alan K.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Protocol for community‐created public MS/MS reference spectra within the Global Natural Products Social Molecular Networking infrastructure</atitle><jtitle>Rapid communications in mass spectrometry</jtitle><addtitle>Rapid Commun Mass Spectrom</addtitle><date>2020-05-30</date><risdate>2020</risdate><volume>34</volume><issue>10</issue><spage>e8725</spage><epage>n/a</epage><pages>e8725-n/a</pages><issn>0951-4198</issn><eissn>1097-0231</eissn><abstract>Rationale
A major hurdle in identifying chemicals in mass spectrometry experiments is the availability of tandem mass spectrometry (MS/MS) reference spectra in public databases. Currently, scientists purchase databases or use public databases such as Global Natural Products Social Molecular Networking (GNPS). The MSMS‐Chooser workflow is an open‐source protocol for the creation of MS/MS reference spectra directly in the GNPS infrastructure.
Methods
An MSMS‐Chooser Sample Template is provided and completed manually. The MSMS‐Chooser Submission File and Sequence Table for data acquisition were programmatically generated. Standards from the Mass Spectrometry Metabolite Library (MSMLS) suspended in a methanol–water (1:1) solution were analyzed. Flow injection on an LC/MS/MS system was used to generate negative and positive mode data using data‐dependent acquisition. The MS/MS spectra and Submission File were uploaded to MSMS‐Chooser workflow in GNPS for automatic selection of MS/MS spectra.
Results
Data acquisition and processing required ~2 h and ~2 min, respectively, per 96‐well plate using MSMS‐Chooser. Analysis of the MSMLS, over 600 small molecules, using MSMS‐Chooser added 889 spectra (including multiple adducts) to the public library in GNPS. Manual validation of one plate indicated accurate selection of MS/MS scans (true positive rate of 0.96 and a true negative rate of 0.99). The MSMS‐Chooser output includes a table formatted for inclusion in the GNPS library as well as the ability to directly launch searches via MASST.
Conclusions
MSMS‐Chooser enables rapid data acquisition, data analysis (selection of MS/MS spectra), and a formatted table for inspection and upload to GNPS. Open file‐format data (.mzML or.mzXML) from most mass spectrometry platforms containing MS/MS spectra can be processed using MSMS‐Chooser. MSMS‐Chooser democratizes the creation of MS/MS reference spectra in GNPS which will improve annotation and strengthen the tools which use the annotation information.</abstract><cop>England</cop><pub>Wiley Subscription Services, Inc</pub><pmid>31930757</pmid><doi>10.1002/rcm.8725</doi><tpages>7</tpages><orcidid>https://orcid.org/0000-0003-1064-8153</orcidid><orcidid>https://orcid.org/0000-0002-0016-8132</orcidid><orcidid>https://orcid.org/0000-0001-5499-2728</orcidid><orcidid>https://orcid.org/0000-0002-3003-1030</orcidid><orcidid>https://orcid.org/0000-0001-5847-2439</orcidid><orcidid>https://orcid.org/0000-0001-7647-6097</orcidid><orcidid>https://orcid.org/0000-0002-2228-6308</orcidid></addata></record> |
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| identifier | ISSN: 0951-4198 |
| ispartof | Rapid communications in mass spectrometry, 2020-05, Vol.34 (10), p.e8725-n/a |
| issn | 0951-4198 1097-0231 |
| language | eng |
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| source | Wiley Online Library Journals Frontfile Complete |
| subjects | Adducts Annotations Data analysis Infrastructure Inspection Libraries Mass spectrometry Metabolites Natural products Scientific imaging Spectra Spectroscopy Workflow |
| title | Protocol for community‐created public MS/MS reference spectra within the Global Natural Products Social Molecular Networking infrastructure |
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