Grouping of complex substances using analytical chemistry data: A framework for quantitative evaluation and visualization.
A detailed characterization of the chemical composition of complex substances, such as products of petroleum refining and environmental mixtures, is greatly needed in exposure assessment and manufacturing. The inherent complexity and variability in the composition of complex substances obfuscate the...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2019-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0223517 |
| _version_ | 1818824984163778560 |
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| author | Melis Onel Burcu Beykal Kyle Ferguson Weihsueh A Chiu Thomas J McDonald Lan Zhou John S House Fred A Wright David A Sheen Ivan Rusyn Efstratios N Pistikopoulos |
| author_facet | Melis Onel Burcu Beykal Kyle Ferguson Weihsueh A Chiu Thomas J McDonald Lan Zhou John S House Fred A Wright David A Sheen Ivan Rusyn Efstratios N Pistikopoulos |
| author_sort | Melis Onel |
| collection | DOAJ |
| description | A detailed characterization of the chemical composition of complex substances, such as products of petroleum refining and environmental mixtures, is greatly needed in exposure assessment and manufacturing. The inherent complexity and variability in the composition of complex substances obfuscate the choices for their detailed analytical characterization. Yet, in lieu of exact chemical composition of complex substances, evaluation of the degree of similarity is a sensible path toward decision-making in environmental health regulations. Grouping of similar complex substances is a challenge that can be addressed via advanced analytical methods and streamlined data analysis and visualization techniques. Here, we propose a framework with unsupervised and supervised analyses to optimally group complex substances based on their analytical features. We test two data sets of complex oil-derived substances. The first data set is from gas chromatography-mass spectrometry (GC-MS) analysis of 20 Standard Reference Materials representing crude oils and oil refining products. The second data set consists of 15 samples of various gas oils analyzed using three analytical techniques: GC-MS, GC×GC-flame ionization detection (FID), and ion mobility spectrometry-mass spectrometry (IM-MS). We use hierarchical clustering using Pearson correlation as a similarity metric for the unsupervised analysis and build classification models using the Random Forest algorithm for the supervised analysis. We present a quantitative comparative assessment of clustering results via Fowlkes-Mallows index, and classification results via model accuracies in predicting the group of an unknown complex substance. We demonstrate the effect of (i) different grouping methodologies, (ii) data set size, and (iii) dimensionality reduction on the grouping quality, and (iv) different analytical techniques on the characterization of the complex substances. While the complexity and variability in chemical composition are an inherent feature of complex substances, we demonstrate how the choices of the data analysis and visualization methods can impact the communication of their characteristics to delineate sufficient similarity. |
| first_indexed | 2024-12-19T00:04:33Z |
| format | Article |
| id | doaj.art-a3ca8acc301341559b33c779ebc27731 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-19T00:04:33Z |
| publishDate | 2019-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-a3ca8acc301341559b33c779ebc277312022-12-21T20:46:18ZengPublic Library of Science (PLoS)PLoS ONE1932-62032019-01-011410e022351710.1371/journal.pone.0223517Grouping of complex substances using analytical chemistry data: A framework for quantitative evaluation and visualization.Melis OnelBurcu BeykalKyle FergusonWeihsueh A ChiuThomas J McDonaldLan ZhouJohn S HouseFred A WrightDavid A SheenIvan RusynEfstratios N PistikopoulosA detailed characterization of the chemical composition of complex substances, such as products of petroleum refining and environmental mixtures, is greatly needed in exposure assessment and manufacturing. The inherent complexity and variability in the composition of complex substances obfuscate the choices for their detailed analytical characterization. Yet, in lieu of exact chemical composition of complex substances, evaluation of the degree of similarity is a sensible path toward decision-making in environmental health regulations. Grouping of similar complex substances is a challenge that can be addressed via advanced analytical methods and streamlined data analysis and visualization techniques. Here, we propose a framework with unsupervised and supervised analyses to optimally group complex substances based on their analytical features. We test two data sets of complex oil-derived substances. The first data set is from gas chromatography-mass spectrometry (GC-MS) analysis of 20 Standard Reference Materials representing crude oils and oil refining products. The second data set consists of 15 samples of various gas oils analyzed using three analytical techniques: GC-MS, GC×GC-flame ionization detection (FID), and ion mobility spectrometry-mass spectrometry (IM-MS). We use hierarchical clustering using Pearson correlation as a similarity metric for the unsupervised analysis and build classification models using the Random Forest algorithm for the supervised analysis. We present a quantitative comparative assessment of clustering results via Fowlkes-Mallows index, and classification results via model accuracies in predicting the group of an unknown complex substance. We demonstrate the effect of (i) different grouping methodologies, (ii) data set size, and (iii) dimensionality reduction on the grouping quality, and (iv) different analytical techniques on the characterization of the complex substances. While the complexity and variability in chemical composition are an inherent feature of complex substances, we demonstrate how the choices of the data analysis and visualization methods can impact the communication of their characteristics to delineate sufficient similarity.https://doi.org/10.1371/journal.pone.0223517 |
| spellingShingle | Melis Onel Burcu Beykal Kyle Ferguson Weihsueh A Chiu Thomas J McDonald Lan Zhou John S House Fred A Wright David A Sheen Ivan Rusyn Efstratios N Pistikopoulos Grouping of complex substances using analytical chemistry data: A framework for quantitative evaluation and visualization. PLoS ONE |
| title | Grouping of complex substances using analytical chemistry data: A framework for quantitative evaluation and visualization. |
| title_full | Grouping of complex substances using analytical chemistry data: A framework for quantitative evaluation and visualization. |
| title_fullStr | Grouping of complex substances using analytical chemistry data: A framework for quantitative evaluation and visualization. |
| title_full_unstemmed | Grouping of complex substances using analytical chemistry data: A framework for quantitative evaluation and visualization. |
| title_short | Grouping of complex substances using analytical chemistry data: A framework for quantitative evaluation and visualization. |
| title_sort | grouping of complex substances using analytical chemistry data a framework for quantitative evaluation and visualization |
| url | https://doi.org/10.1371/journal.pone.0223517 |
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