Predicting compound amenability with liquid chromatography-mass spectrometry to improve non-targeted analysis
The dataset and experimental and predicted amenability calls are provided in the supplemental file “Supplemental_ToxCast_PhaseII.xlsx”.
PaDEL descriptors were generated for each candidate and amenability predictions were calculated using both ESI+ and ESI- downsampled models. The resulting dataset is available in the supplemental file “Supplemental_Application.xlsx”.
It should be noted that the dataset used in this demonstration is biased toward environmentally relevant chemicals, many of which appear in a large number of chemical lists on the Dashboard (see the DATA_SOURCES column in “Supplemental_Application.xlsx” for both ESI+ and ESI-).
Training and test datasets were constructed using the PaDEL descriptors and the ESI+ and ESI- endpoint values discussed previously. These training and test sets are provided in the supplemental file “Supplemental_train_test.xlsx”.
A list of descriptors is provided in the supplemental file “Supplemental_Descriptors.xlsx”.
A similar plot (Figure S1) of variable importance for the ESI+ upsampled model, and a similar plot (Figure S2) of variable importance for the ESI- upsampled model can be found in “Supplemental_Figures.docx”.
This dataset is associated with the following publication:
Lowe, C., K. Isaacs, A. McEachran, C. Grulke, J. Sobus, E. Ulrich, A. Richard, A. Chao, J. Wambaugh, and A. Williams. Predicting compound amenability with liquid chromatography-mass spectrometry to improve non-targeted analysis. Analytical and Bioanalytical Chemistry. Springer, New York, NY, USA, 413(30): 7495-7508, (2021).
Resources
5 resources available
-
Supplemental_Application.xlsx
APPLICATION/VND.OPENXMLFORMATS-OFFICEDOCUMENT.SPREADSHEETML.SHEET -
Supplemental_Descriptors.xlsx
APPLICATION/VND.OPENXMLFORMATS-OFFICEDOCUMENT.SPREADSHEETML.SHEET -
Supplemental_Figures.docx
APPLICATION/VND.OPENXMLFORMATS-OFFICEDOCUMENT.WORDPROCESSINGML.DOCUMENT -
Supplemental_ToxCast_PhaseII.xlsx
APPLICATION/VND.OPENXMLFORMATS-OFFICEDOCUMENT.SPREADSHEETML.SHEET -
Supplemental_train_test.xlsx
APPLICATION/VND.OPENXMLFORMATS-OFFICEDOCUMENT.SPREADSHEETML.SHEET
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Complete Metadata
| @type | dcat:Dataset |
|---|---|
| accessLevel | public |
| bureauCode |
[ "020:00" ] |
| contactPoint |
{ "fn": "Antony Williams", "hasEmail": "mailto:williams.antony@epa.gov" } |
| description | The dataset and experimental and predicted amenability calls are provided in the supplemental file “Supplemental_ToxCast_PhaseII.xlsx”. PaDEL descriptors were generated for each candidate and amenability predictions were calculated using both ESI+ and ESI- downsampled models. The resulting dataset is available in the supplemental file “Supplemental_Application.xlsx”. It should be noted that the dataset used in this demonstration is biased toward environmentally relevant chemicals, many of which appear in a large number of chemical lists on the Dashboard (see the DATA_SOURCES column in “Supplemental_Application.xlsx” for both ESI+ and ESI-). Training and test datasets were constructed using the PaDEL descriptors and the ESI+ and ESI- endpoint values discussed previously. These training and test sets are provided in the supplemental file “Supplemental_train_test.xlsx”. A list of descriptors is provided in the supplemental file “Supplemental_Descriptors.xlsx”. A similar plot (Figure S1) of variable importance for the ESI+ upsampled model, and a similar plot (Figure S2) of variable importance for the ESI- upsampled model can be found in “Supplemental_Figures.docx”. This dataset is associated with the following publication: Lowe, C., K. Isaacs, A. McEachran, C. Grulke, J. Sobus, E. Ulrich, A. Richard, A. Chao, J. Wambaugh, and A. Williams. Predicting compound amenability with liquid chromatography-mass spectrometry to improve non-targeted analysis. Analytical and Bioanalytical Chemistry. Springer, New York, NY, USA, 413(30): 7495-7508, (2021). |
| distribution |
[ { "title": "Supplemental_Application.xlsx", "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", "downloadURL": "https://pasteur.epa.gov/uploads/10.23719/1524095/Supplemental_Application.xlsx" }, { "title": "Supplemental_Descriptors.xlsx", "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", "downloadURL": "https://pasteur.epa.gov/uploads/10.23719/1524095/Supplemental_Descriptors.xlsx" }, { "title": "Supplemental_Figures.docx", "mediaType": "application/vnd.openxmlformats-officedocument.wordprocessingml.document", "downloadURL": "https://pasteur.epa.gov/uploads/10.23719/1524095/Supplemental_Figures.docx" }, { "title": "Supplemental_ToxCast_PhaseII.xlsx", "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", "downloadURL": "https://pasteur.epa.gov/uploads/10.23719/1524095/Supplemental_ToxCast_PhaseII.xlsx" }, { "title": "Supplemental_train_test.xlsx", "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", "downloadURL": "https://pasteur.epa.gov/uploads/10.23719/1524095/Supplemental_train_test.xlsx" } ] |
| identifier | https://doi.org/10.23719/1524095 |
| keyword |
[ "Predictive Modeling", "Suspect Screening Analysis", "machine learning", "mass spectrometry", "non-targeted analysis", "random forest" ] |
| license | https://pasteur.epa.gov/license/sciencehub-license.html |
| modified | 2021-06-03 |
| programCode |
[ "020:000" ] |
| publisher |
{ "name": "U.S. EPA Office of Research and Development (ORD)", "subOrganizationOf": { "name": "U.S. Environmental Protection Agency", "subOrganizationOf": { "name": "U.S. Government" } } } |
| references |
[ "https://doi.org/10.1007/s00216-021-03713-w" ] |
| rights |
null
|
| title | Predicting compound amenability with liquid chromatography-mass spectrometry to improve non-targeted analysis |
