Creation and filtering of a recurrent spectral library of CHO cell metabolites and media components
This paper reports the first implementation of a new type of mass spectral library for the analysis of Chinese hamster ovary (CHO) cell metabolites that allows users to quickly identify most compounds in any complex metabolite sample. We also describe an annotation methodology developed to filter ou...
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| Veröffentlicht in: | Biotechnology and bioengineering 2021-04, Vol.118 (4), p.1491-1510 |
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| creator | Telu, Kelly H. Marupaka, Ramesh Andriamaharavo, Nirina R. Simón‐Manso, Yamil Liang, Yuxue Mirokhin, Yuri A. Bukhari, Tallat H. Preston, Renae J. Kashi, Lila Kelman, Zvi Stein, Stephen E. |
| description | This paper reports the first implementation of a new type of mass spectral library for the analysis of Chinese hamster ovary (CHO) cell metabolites that allows users to quickly identify most compounds in any complex metabolite sample. We also describe an annotation methodology developed to filter out artifacts and low‐quality spectra from recurrent unidentified spectra of metabolites. CHO cells are commonly used to produce biological therapeutics. Metabolic profiles of CHO cells and media can be used to monitor process variability and look for markers that discriminate between batches of product. We have created a comprehensive library of both identified and unidentified metabolites derived from CHO cells that can be used in conjunction with tandem mass spectrometry to identify metabolites. In addition, we present a workflow that can be used for assigning confidence to a NIST MS/MS Library search match based on prior probability of general utility. The goal of our work is to annotate and identify (when possible), all liquid chromatography‐mass spectrometry generated metabolite ions as well as create automatable library building and identification pipelines for use by others in the field.
A freely available mass spectral library composed of identified and unidentified recurrent spectra from the analysis of Chinese hamster ovary (CHO) cell metabolites has been created. The comprehensive library of metabolites can be used in conjunction with tandem mass spectrometry to quickly identify compounds in a complex metabolite sample. An annotation strategy to filter out background, artifacts, and low‐quality spectra from recurrent unidentified spectra of metabolites was also developed. |
| doi_str_mv | 10.1002/bit.27661 |
| format | Article |
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A freely available mass spectral library composed of identified and unidentified recurrent spectra from the analysis of Chinese hamster ovary (CHO) cell metabolites has been created. The comprehensive library of metabolites can be used in conjunction with tandem mass spectrometry to quickly identify compounds in a complex metabolite sample. An annotation strategy to filter out background, artifacts, and low‐quality spectra from recurrent unidentified spectra of metabolites was also developed.</description><identifier>ISSN: 0006-3592</identifier><identifier>EISSN: 1097-0290</identifier><identifier>DOI: 10.1002/bit.27661</identifier><identifier>PMID: 33404064</identifier><language>eng</language><publisher>United States: Wiley Subscription Services, Inc</publisher><subject>Animals ; Annotations ; Chinese hamster ovary cells ; CHO Cells ; Conditional probability ; Cricetulus ; Culture Media - chemistry ; global metabolite profiling ; Libraries ; Liquid chromatography ; liquid chromatography‐tandem mass spectrometry ; Mass spectrometry ; Mass spectroscopy ; Metabolites ; Metabolome ; Metabolomics ; nontargeted metabolomics ; recurrent unidentified spectra ; Scientific imaging ; Small Molecule Libraries ; Spectra ; Spectroscopy ; Toxicity ; Workflow</subject><ispartof>Biotechnology and bioengineering, 2021-04, Vol.118 (4), p.1491-1510</ispartof><rights>2021 The Authors. Published by Wiley Periodicals LLC. This article has been contributed to by US Government employees and their work is in the public domain in the USA</rights><rights>2021 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals LLC. This article has been contributed to by US Government employees and their work is in the public domain in the USA.</rights><rights>2021. This article is published under http://creativecommons.org/licenses/by-nc/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4801-41af7fbd638bb8f3b61866ab5abd4e5379eb0853a94052c56527011187acc46a3</citedby><cites>FETCH-LOGICAL-c4801-41af7fbd638bb8f3b61866ab5abd4e5379eb0853a94052c56527011187acc46a3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fbit.27661$$EPDF$$P50$$Gwiley$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fbit.27661$$EHTML$$P50$$Gwiley$$Hfree_for_read</linktohtml><link.rule.ids>230,314,776,780,881,1411,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33404064$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Telu, Kelly H.</creatorcontrib><creatorcontrib>Marupaka, Ramesh</creatorcontrib><creatorcontrib>Andriamaharavo, Nirina R.</creatorcontrib><creatorcontrib>Simón‐Manso, Yamil</creatorcontrib><creatorcontrib>Liang, Yuxue</creatorcontrib><creatorcontrib>Mirokhin, Yuri A.</creatorcontrib><creatorcontrib>Bukhari, Tallat H.</creatorcontrib><creatorcontrib>Preston, Renae J.</creatorcontrib><creatorcontrib>Kashi, Lila</creatorcontrib><creatorcontrib>Kelman, Zvi</creatorcontrib><creatorcontrib>Stein, Stephen E.</creatorcontrib><title>Creation and filtering of a recurrent spectral library of CHO cell metabolites and media components</title><title>Biotechnology and bioengineering</title><addtitle>Biotechnol Bioeng</addtitle><description>This paper reports the first implementation of a new type of mass spectral library for the analysis of Chinese hamster ovary (CHO) cell metabolites that allows users to quickly identify most compounds in any complex metabolite sample. We also describe an annotation methodology developed to filter out artifacts and low‐quality spectra from recurrent unidentified spectra of metabolites. CHO cells are commonly used to produce biological therapeutics. Metabolic profiles of CHO cells and media can be used to monitor process variability and look for markers that discriminate between batches of product. We have created a comprehensive library of both identified and unidentified metabolites derived from CHO cells that can be used in conjunction with tandem mass spectrometry to identify metabolites. In addition, we present a workflow that can be used for assigning confidence to a NIST MS/MS Library search match based on prior probability of general utility. The goal of our work is to annotate and identify (when possible), all liquid chromatography‐mass spectrometry generated metabolite ions as well as create automatable library building and identification pipelines for use by others in the field.
A freely available mass spectral library composed of identified and unidentified recurrent spectra from the analysis of Chinese hamster ovary (CHO) cell metabolites has been created. The comprehensive library of metabolites can be used in conjunction with tandem mass spectrometry to quickly identify compounds in a complex metabolite sample. An annotation strategy to filter out background, artifacts, and low‐quality spectra from recurrent unidentified spectra of metabolites was also developed.</description><subject>Animals</subject><subject>Annotations</subject><subject>Chinese hamster ovary cells</subject><subject>CHO Cells</subject><subject>Conditional probability</subject><subject>Cricetulus</subject><subject>Culture Media - chemistry</subject><subject>global metabolite profiling</subject><subject>Libraries</subject><subject>Liquid chromatography</subject><subject>liquid chromatography‐tandem mass spectrometry</subject><subject>Mass spectrometry</subject><subject>Mass spectroscopy</subject><subject>Metabolites</subject><subject>Metabolome</subject><subject>Metabolomics</subject><subject>nontargeted metabolomics</subject><subject>recurrent unidentified spectra</subject><subject>Scientific imaging</subject><subject>Small Molecule Libraries</subject><subject>Spectra</subject><subject>Spectroscopy</subject><subject>Toxicity</subject><subject>Workflow</subject><issn>0006-3592</issn><issn>1097-0290</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>24P</sourceid><sourceid>EIF</sourceid><recordid>eNp1kc1KJDEUhYM4aPuz8AUk4GZclN6k8lcbwWmcURDcOOuQpFMaqaq0SZXi25u2HXEEVyHcLyff5SB0QOCEANBTG8YTKoUgG2hGoJEV0AY20QwARFXzhm6jnZwfylUqIbbQdl0zYCDYDLl58mYMccBmWOA2dKNPYbjDscUGJ--mlPww4rz0bkymw12wyaSX1Xx-eYOd7zrc-9HY2IXR57eU3i-CwS72yziUx3kP_WhNl_3--7mL_v6-uJ1fVtc3f67m59eVYwpIxYhpZWsXolbWqra2ghRbY7mxC-Z5LRtvQfHaNAw4dVxwKoEQoqRxjglT76Kzde5yssXBlb-Lsl6m0BdlHU3Q_0-GcK_v4pNWwBSTUAJ-vgek-Dj5POo-5NWKZvBxypoyyTlVjIuCHn1BH-KUhrKephyKkxJNU6jjNeVSzDn59kOGgF5Vp0t1-q26wh5-tv8g_3VVgNM18Bw6__J9kv51dbuOfAVKLaN0</recordid><startdate>202104</startdate><enddate>202104</enddate><creator>Telu, Kelly H.</creator><creator>Marupaka, Ramesh</creator><creator>Andriamaharavo, Nirina R.</creator><creator>Simón‐Manso, Yamil</creator><creator>Liang, Yuxue</creator><creator>Mirokhin, Yuri A.</creator><creator>Bukhari, Tallat H.</creator><creator>Preston, Renae J.</creator><creator>Kashi, Lila</creator><creator>Kelman, Zvi</creator><creator>Stein, Stephen E.</creator><general>Wiley Subscription Services, Inc</general><general>John Wiley and Sons Inc</general><scope>24P</scope><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>7QF</scope><scope>7QO</scope><scope>7QQ</scope><scope>7SC</scope><scope>7SE</scope><scope>7SP</scope><scope>7SR</scope><scope>7T7</scope><scope>7TA</scope><scope>7TB</scope><scope>7U5</scope><scope>8BQ</scope><scope>8FD</scope><scope>C1K</scope><scope>F28</scope><scope>FR3</scope><scope>H8D</scope><scope>H8G</scope><scope>JG9</scope><scope>JQ2</scope><scope>KR7</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>P64</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>202104</creationdate><title>Creation and filtering of a recurrent spectral library of CHO cell metabolites and media components</title><author>Telu, Kelly H. ; 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We also describe an annotation methodology developed to filter out artifacts and low‐quality spectra from recurrent unidentified spectra of metabolites. CHO cells are commonly used to produce biological therapeutics. Metabolic profiles of CHO cells and media can be used to monitor process variability and look for markers that discriminate between batches of product. We have created a comprehensive library of both identified and unidentified metabolites derived from CHO cells that can be used in conjunction with tandem mass spectrometry to identify metabolites. In addition, we present a workflow that can be used for assigning confidence to a NIST MS/MS Library search match based on prior probability of general utility. The goal of our work is to annotate and identify (when possible), all liquid chromatography‐mass spectrometry generated metabolite ions as well as create automatable library building and identification pipelines for use by others in the field.
A freely available mass spectral library composed of identified and unidentified recurrent spectra from the analysis of Chinese hamster ovary (CHO) cell metabolites has been created. The comprehensive library of metabolites can be used in conjunction with tandem mass spectrometry to quickly identify compounds in a complex metabolite sample. An annotation strategy to filter out background, artifacts, and low‐quality spectra from recurrent unidentified spectra of metabolites was also developed.</abstract><cop>United States</cop><pub>Wiley Subscription Services, Inc</pub><pmid>33404064</pmid><doi>10.1002/bit.27661</doi><tpages>20</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | Biotechnology and bioengineering, 2021-04, Vol.118 (4), p.1491-1510 |
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| source | MEDLINE; Wiley Online Library Journals Frontfile Complete |
| subjects | Animals Annotations Chinese hamster ovary cells CHO Cells Conditional probability Cricetulus Culture Media - chemistry global metabolite profiling Libraries Liquid chromatography liquid chromatography‐tandem mass spectrometry Mass spectrometry Mass spectroscopy Metabolites Metabolome Metabolomics nontargeted metabolomics recurrent unidentified spectra Scientific imaging Small Molecule Libraries Spectra Spectroscopy Toxicity Workflow |
| title | Creation and filtering of a recurrent spectral library of CHO cell metabolites and media components |
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