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Shift‐invariant tri‐linearity—A new model for resolving untargeted gas chromatography coupled mass spectrometry data
Multi‐way data analysis is popular in chemometrics for the decomposition of, for example, spectroscopic or chromatographic higher‐order tensor datasets. Parallel factor analysis (PARAFAC) and its extension, PARAFAC2, are extensively employed methods in chemometrics. Applications of PARAFAC2 for unta...
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| Published in: | Journal of chemometrics 2023-08, Vol.37 (8), p.n/a |
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| creator | Schneide, Paul‐Albert Bro, Rasmus Gallagher, Neal B. |
| description | Multi‐way data analysis is popular in chemometrics for the decomposition of, for example, spectroscopic or chromatographic higher‐order tensor datasets. Parallel factor analysis (PARAFAC) and its extension, PARAFAC2, are extensively employed methods in chemometrics. Applications of PARAFAC2 for untargeted data analysis of hyphenated gas chromatography coupled with mass spectrometric detection (GC‐MS) have proven to be very successful. This is attributable to the ability of PARAFAC2 to account for retention time shifts and shape changes in chromatographic elution profiles. Despite its usefulness, the most common implementations of PARAFAC2 are considered quite slow. Furthermore, it is difficult to apply constraints (e.g., non‐negativity) to the shifted mode in PARAFAC2 models. Both aspects are addressed by a new shift‐invariant tri‐linearity (SIT) algorithm proposed in this paper. It is shown on simulated and real GC‐MS data that the SIT algorithm is 20–60 times faster than the latest PARAFAC2‐alternating least squares (ALS) implementation and the PARAFAC2‐flexible coupling algorithm. Further, the SIT method allows the implementation of constraints in all modes. Trials on real‐world data indicate that the SIT algorithm compares well with alternatives. The new SIT method achieves better factor resolution than the benchmark in some cases and tends to need fewer latent variables to extract the same chemical information. Although SIT is not capable of modeling shape changes in elution profiles, trials on real‐world data indicate the great robustness of the method even in those cases.
A new shift‐invariant tri‐linearity algorithm for the analysis of untargeted gas chromatography coupled mass spectrometry data is presented. The algorithm performs significantly better than the benchmark in terms of computational efficiency and provides excellent results in terms of factor resolution. Simulated and real GC‐MS data have been used for the performance assessment. |
| doi_str_mv | 10.1002/cem.3501 |
| format | article |
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A new shift‐invariant tri‐linearity algorithm for the analysis of untargeted gas chromatography coupled mass spectrometry data is presented. The algorithm performs significantly better than the benchmark in terms of computational efficiency and provides excellent results in terms of factor resolution. Simulated and real GC‐MS data have been used for the performance assessment.</description><identifier>ISSN: 0886-9383</identifier><identifier>EISSN: 1099-128X</identifier><identifier>DOI: 10.1002/cem.3501</identifier><language>eng</language><publisher>Chichester: Wiley Subscription Services, Inc</publisher><subject>Algorithms ; Chemometrics ; Chromatography ; Data analysis ; Elution ; Factor analysis ; Gas chromatography ; Invariants ; Ions ; Linearity ; Mass spectrometry ; Retention time ; Tensors</subject><ispartof>Journal of chemometrics, 2023-08, Vol.37 (8), p.n/a</ispartof><rights>2023 The Authors. published by John Wiley & Sons Ltd.</rights><rights>2023. This article is published under http://creativecommons.org/licenses/by/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-c3271-aa5d0d28357645d18bb150361b81b550f5ebf8366dc49887ce427c213fa480413</citedby><cites>FETCH-LOGICAL-c3271-aa5d0d28357645d18bb150361b81b550f5ebf8366dc49887ce427c213fa480413</cites><orcidid>0000-0002-7641-4854 ; 0000-0002-8365-5699</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%2Fcem.3501$$EPDF$$P50$$Gwiley$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fcem.3501$$EHTML$$P50$$Gwiley$$Hfree_for_read</linktohtml><link.rule.ids>315,786,790,27957,27958,50923,51032</link.rule.ids></links><search><creatorcontrib>Schneide, Paul‐Albert</creatorcontrib><creatorcontrib>Bro, Rasmus</creatorcontrib><creatorcontrib>Gallagher, Neal B.</creatorcontrib><title>Shift‐invariant tri‐linearity—A new model for resolving untargeted gas chromatography coupled mass spectrometry data</title><title>Journal of chemometrics</title><description>Multi‐way data analysis is popular in chemometrics for the decomposition of, for example, spectroscopic or chromatographic higher‐order tensor datasets. Parallel factor analysis (PARAFAC) and its extension, PARAFAC2, are extensively employed methods in chemometrics. Applications of PARAFAC2 for untargeted data analysis of hyphenated gas chromatography coupled with mass spectrometric detection (GC‐MS) have proven to be very successful. This is attributable to the ability of PARAFAC2 to account for retention time shifts and shape changes in chromatographic elution profiles. Despite its usefulness, the most common implementations of PARAFAC2 are considered quite slow. Furthermore, it is difficult to apply constraints (e.g., non‐negativity) to the shifted mode in PARAFAC2 models. Both aspects are addressed by a new shift‐invariant tri‐linearity (SIT) algorithm proposed in this paper. It is shown on simulated and real GC‐MS data that the SIT algorithm is 20–60 times faster than the latest PARAFAC2‐alternating least squares (ALS) implementation and the PARAFAC2‐flexible coupling algorithm. Further, the SIT method allows the implementation of constraints in all modes. Trials on real‐world data indicate that the SIT algorithm compares well with alternatives. The new SIT method achieves better factor resolution than the benchmark in some cases and tends to need fewer latent variables to extract the same chemical information. Although SIT is not capable of modeling shape changes in elution profiles, trials on real‐world data indicate the great robustness of the method even in those cases.
A new shift‐invariant tri‐linearity algorithm for the analysis of untargeted gas chromatography coupled mass spectrometry data is presented. The algorithm performs significantly better than the benchmark in terms of computational efficiency and provides excellent results in terms of factor resolution. Simulated and real GC‐MS data have been used for the performance assessment.</description><subject>Algorithms</subject><subject>Chemometrics</subject><subject>Chromatography</subject><subject>Data analysis</subject><subject>Elution</subject><subject>Factor analysis</subject><subject>Gas chromatography</subject><subject>Invariants</subject><subject>Ions</subject><subject>Linearity</subject><subject>Mass spectrometry</subject><subject>Retention time</subject><subject>Tensors</subject><issn>0886-9383</issn><issn>1099-128X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>24P</sourceid><sourceid>WIN</sourceid><recordid>eNp1kL1OwzAURi0EEqUg8QiWWFhS7DhOnLGqyo9UxABIbJbjOKmrJA62SxWmPgIDT9gnwaWsTFffPUf3Sh8AlxhNMELxjVTthFCEj8AIozyPcMzejsEIMZZGOWHkFJw5t0IoMJKMwOfzUld-t_3S3YewWnQeeqtDbnSnwsIPu-33FHZqA1tTqgZWxkKrnGk-dFfDdeeFrZVXJayFg3JpTSu8qa3olwOUZt03AbXCOeh6JX3AytsBlsKLc3BSicapi785Bq-385fZfbR4unuYTReRJHGGIyFoicqYEZqlCS0xKwpMEUlxwXBBKaqoKipG0rSUSc5YJlUSZzLGpBIJQwkmY3B1uNtb875WzvOVWdsuvOQxSzKc5iRjwbo-WNIa56yqeG91K-zAMeL7Znlolu-bDWp0UDe6UcO_Hp_NH3_9HweGfqY</recordid><startdate>202308</startdate><enddate>202308</enddate><creator>Schneide, Paul‐Albert</creator><creator>Bro, Rasmus</creator><creator>Gallagher, Neal B.</creator><general>Wiley Subscription Services, Inc</general><scope>24P</scope><scope>WIN</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7SC</scope><scope>7U5</scope><scope>8FD</scope><scope>JQ2</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><orcidid>https://orcid.org/0000-0002-7641-4854</orcidid><orcidid>https://orcid.org/0000-0002-8365-5699</orcidid></search><sort><creationdate>202308</creationdate><title>Shift‐invariant tri‐linearity—A new model for resolving untargeted gas chromatography coupled mass spectrometry data</title><author>Schneide, Paul‐Albert ; Bro, Rasmus ; Gallagher, Neal B.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3271-aa5d0d28357645d18bb150361b81b550f5ebf8366dc49887ce427c213fa480413</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Algorithms</topic><topic>Chemometrics</topic><topic>Chromatography</topic><topic>Data analysis</topic><topic>Elution</topic><topic>Factor analysis</topic><topic>Gas chromatography</topic><topic>Invariants</topic><topic>Ions</topic><topic>Linearity</topic><topic>Mass spectrometry</topic><topic>Retention time</topic><topic>Tensors</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Schneide, Paul‐Albert</creatorcontrib><creatorcontrib>Bro, Rasmus</creatorcontrib><creatorcontrib>Gallagher, Neal B.</creatorcontrib><collection>Wiley_OA刊</collection><collection>Wiley Online Library</collection><collection>CrossRef</collection><collection>Computer and Information Systems Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>Technology Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><jtitle>Journal of chemometrics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Schneide, Paul‐Albert</au><au>Bro, Rasmus</au><au>Gallagher, Neal B.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Shift‐invariant tri‐linearity—A new model for resolving untargeted gas chromatography coupled mass spectrometry data</atitle><jtitle>Journal of chemometrics</jtitle><date>2023-08</date><risdate>2023</risdate><volume>37</volume><issue>8</issue><epage>n/a</epage><issn>0886-9383</issn><eissn>1099-128X</eissn><abstract>Multi‐way data analysis is popular in chemometrics for the decomposition of, for example, spectroscopic or chromatographic higher‐order tensor datasets. 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Further, the SIT method allows the implementation of constraints in all modes. Trials on real‐world data indicate that the SIT algorithm compares well with alternatives. The new SIT method achieves better factor resolution than the benchmark in some cases and tends to need fewer latent variables to extract the same chemical information. Although SIT is not capable of modeling shape changes in elution profiles, trials on real‐world data indicate the great robustness of the method even in those cases.
A new shift‐invariant tri‐linearity algorithm for the analysis of untargeted gas chromatography coupled mass spectrometry data is presented. The algorithm performs significantly better than the benchmark in terms of computational efficiency and provides excellent results in terms of factor resolution. Simulated and real GC‐MS data have been used for the performance assessment.</abstract><cop>Chichester</cop><pub>Wiley Subscription Services, Inc</pub><doi>10.1002/cem.3501</doi><tpages>20</tpages><orcidid>https://orcid.org/0000-0002-7641-4854</orcidid><orcidid>https://orcid.org/0000-0002-8365-5699</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Algorithms Chemometrics Chromatography Data analysis Elution Factor analysis Gas chromatography Invariants Ions Linearity Mass spectrometry Retention time Tensors |
| title | Shift‐invariant tri‐linearity—A new model for resolving untargeted gas chromatography coupled mass spectrometry data |
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