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 |
