Summary of Study ST001807
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001141. The data can be accessed directly via it's Project DOI: 10.21228/M8711S This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST001807 |
| Study Title | Untargeted metabolomics of Daphnia magna exposed to a lithium cobalt oxide nanomaterial |
| Study Type | Untargeted MS |
| Study Summary | The goal of this project was to determine lithium cobalt oxide (LCO)’s effects on pathways in the model organism Daphnia magna through untargeted metabolomics. |
| Institute | University of Wisconsin - Milwaukee |
| Department | School of Freshwater Sciences |
| Laboratory | Rebecca Klaper |
| Last Name | Klaper |
| First Name | Rebecca |
| Address | 600 E Greenfield Ave, Milwaukee, WI 53204 |
| rklaper@uwm.edu | |
| Phone | 4143821713 |
| Submit Date | 2021-05-18 |
| Num Groups | 4 |
| Total Subjects | 36 |
| Study Comments | Pooled samples of 20 Daphnia magna per replicate. |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | MS(Dir. Inf.) |
| Release Date | 2022-05-19 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN002929 | AN002930 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | None (Direct infusion) | None (Direct infusion) |
| Chromatography system | LTQ Orbitrap Elite (Thermo Fisher Scientific) | LTQ Orbitrap Elite (Thermo Fisher Scientific) |
| Column | none | none |
| MS Type | ESI | ESI |
| MS instrument type | LTQ-FT | LTQ-FT |
| MS instrument name | Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap | Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | arbitrary units | arbitrary units |
MS:
| MS ID: | MS002720 |
| Analysis ID: | AN002929 |
| Instrument Name: | Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap |
| Instrument Type: | LTQ-FT |
| MS Type: | ESI |
| MS Comments: | For both positive and negative ion analyses, samples were randomized and 5 µL of sample supernatant was pipetted into a pre-washed 96-well sample plate in quadruplicate. Three quality control (QC) samples (a mixture with equal volume from all samples) and a blank were also included on each plate. Loaded plates were covered with a foil seal using heat sealer and loaded into a TriVersa Nano-Mate® nanoelectro-spray ion source (Advion) with the cooler set at 10 ºC. Non-targeted analysis was carried out on polar fractions by direct infusion mass spectrometry (DIMS) using an LTQ Orbitrap Elite (Thermo Fisher Scientific). 21 overlapping selected ion monitoring (SIM) windows were collected covering m/z values from 50 to 620. Data are available in the NIH National Metabolomics Data Repository (NMDR). The Galaxy pipeline at the University of Birmingham was used to process raw data collected. SIM windows were assembled into single spectra for each sample (SIM-Stitching). Filtering A signal to noise ratio (SNR) of 10 was selected to filter out background noise from the data. A replicate filter was applied to retain only peaks found in at least 3 out of 4 technical replicates, and samples aligned across biological samples. A blank filter was applied to only retain peaks if they are a specified % larger than blank values. Finally a sample filter was applied to keep only those peaks found in greater than 80% of biological samples. Missing-value imputation, normalization, and quality assessment Probabilistic quotient normalization (PQN) was applied to normalize the DIMS metabolomics data to account for differences in dilution between samples. A K-nearest neighbor (KNN) algorithm was then applied to impute missing values. A generalized-log transformation was then applied to stabilize the technical variance of the DIMS measurements. To assess data quality, the median relative standard deviation (RSD) was measured across technical replicates and an RSD cutoff value of 10 was specified. Data analysis Univariate ANOVAs were carried out on metabolite data with a false discovery rate (FDR) correction to account for the large number of possible comparisons. Peaks were annotated using the Functional Analysis tool for MS peaks on the MetaboAnalyst 5.0 online web server.4 Peak list files were uploaded containing m/z values and FDR corrected p-values obtained by the processing above, and analyzed in the respective (positive or negative) ion mode with a 5.0 ppm mass tolerance. For enrichment analysis, the Mummichog algorithm was applied with a p-value cutoff of p < 0.1 and analyzed against the KEGG database for Homo sapiens and Drosophila melanogaster. References (1) Bozich, J.; Hang, M.; Hamers, R.; Klaper, R. Core Chemistry Influences the Toxicity of Multicomponent Metal Oxide Nanomaterials, Lithium Nickel Manganese Cobalt Oxide, and Lithium Cobalt Oxide to Daphnia Magna. Environ. Toxicol. Chem. 2017, 36 (9), 2493–2502. https://doi.org/10.1002/etc.3791. (2) Niemuth, N. J. N. J.; Curtis, B. J. B. J.; Hang, M. N. M. N.; Gallagher, M. J. M. J.; Fairbrother, D. H. H.; Hamers, R. J. R. J.; Klaper, R. D. R. D. Next-Generation Complex Metal Oxide Nanomaterials Negatively Impact Growth and Development in the Benthic Invertebrate Chironomus Riparius upon Settling. Environ. Sci. Technol. 2019, 53 (7), 3860–3870. https://doi.org/10.1021/acs.est.8b06804. (3) Davidson, R. L.; Weber, R. J. M.; Liu, H.; Sharma-Oates, A.; Viant, M. R. Galaxy-M: A Galaxy Workflow for Processing and Analyzing Direct Infusion and Liquid Chromatography Mass Spectrometry-Based Metabolomics Data. Gigascience 2016, 5 (1), 10. https://doi.org/10.1186/s13742-016-0115-8. (4) Xia, J.; Psychogios, N.; Young, N.; Wishart, D. S. MetaboAnalyst: A Web Server for Metabolomic Data Analysis and Interpretation. Nucleic Acids Res. 2009, 37 (Web Server), W652–W660. https://doi.org/10.1093/nar/gkp356. |
| Ion Mode: | POSITIVE |
| MS ID: | MS002721 |
| Analysis ID: | AN002930 |
| Instrument Name: | Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap |
| Instrument Type: | LTQ-FT |
| MS Type: | ESI |
| MS Comments: | For both positive and negative ion analyses, samples were randomized and 5 µL of sample supernatant was pipetted into a pre-washed 96-well sample plate in quadruplicate. Three quality control (QC) samples (a mixture with equal volume from all samples) and a blank were also included on each plate. Loaded plates were covered with a foil seal using heat sealer and loaded into a TriVersa Nano-Mate® nanoelectro-spray ion source (Advion) with the cooler set at 10 ºC. Non-targeted analysis was carried out on polar fractions by direct infusion mass spectrometry (DIMS) using an LTQ Orbitrap Elite (Thermo Fisher Scientific). 21 overlapping selected ion monitoring (SIM) windows were collected covering m/z values from 50 to 620. Data are available in the NIH National Metabolomics Data Repository (NMDR). The Galaxy pipeline at the University of Birmingham was used to process raw data collected. SIM windows were assembled into single spectra for each sample (SIM-Stitching). Filtering A signal to noise ratio (SNR) of 10 was selected to filter out background noise from the data. A replicate filter was applied to retain only peaks found in at least 3 out of 4 technical replicates, and samples aligned across biological samples. A blank filter was applied to only retain peaks if they are a specified % larger than blank values. Finally a sample filter was applied to keep only those peaks found in greater than 80% of biological samples. Missing-value imputation, normalization, and quality assessment Probabilistic quotient normalization (PQN) was applied to normalize the DIMS metabolomics data to account for differences in dilution between samples. A K-nearest neighbor (KNN) algorithm was then applied to impute missing values. A generalized-log transformation was then applied to stabilize the technical variance of the DIMS measurements. To assess data quality, the median relative standard deviation (RSD) was measured across technical replicates and an RSD cutoff value of 10 was specified. Data analysis Univariate ANOVAs were carried out on metabolite data with a false discovery rate (FDR) correction to account for the large number of possible comparisons. Peaks were annotated using the Functional Analysis tool for MS peaks on the MetaboAnalyst 5.0 online web server.4 Peak list files were uploaded containing m/z values and FDR corrected p-values obtained by the processing above, and analyzed in the respective (positive or negative) ion mode with a 5.0 ppm mass tolerance. For enrichment analysis, the Mummichog algorithm was applied with a p-value cutoff of p < 0.1 and analyzed against the KEGG database for Homo sapiens and Drosophila melanogaster. References (1) Bozich, J.; Hang, M.; Hamers, R.; Klaper, R. Core Chemistry Influences the Toxicity of Multicomponent Metal Oxide Nanomaterials, Lithium Nickel Manganese Cobalt Oxide, and Lithium Cobalt Oxide to Daphnia Magna. Environ. Toxicol. Chem. 2017, 36 (9), 2493–2502. https://doi.org/10.1002/etc.3791. (2) Niemuth, N. J. N. J.; Curtis, B. J. B. J.; Hang, M. N. M. N.; Gallagher, M. J. M. J.; Fairbrother, D. H. H.; Hamers, R. J. R. J.; Klaper, R. D. R. D. Next-Generation Complex Metal Oxide Nanomaterials Negatively Impact Growth and Development in the Benthic Invertebrate Chironomus Riparius upon Settling. Environ. Sci. Technol. 2019, 53 (7), 3860–3870. https://doi.org/10.1021/acs.est.8b06804. (3) Davidson, R. L.; Weber, R. J. M.; Liu, H.; Sharma-Oates, A.; Viant, M. R. Galaxy-M: A Galaxy Workflow for Processing and Analyzing Direct Infusion and Liquid Chromatography Mass Spectrometry-Based Metabolomics Data. Gigascience 2016, 5 (1), 10. https://doi.org/10.1186/s13742-016-0115-8. (4) Xia, J.; Psychogios, N.; Young, N.; Wishart, D. S. MetaboAnalyst: A Web Server for Metabolomic Data Analysis and Interpretation. Nucleic Acids Res. 2009, 37 (Web Server), W652–W660. https://doi.org/10.1093/nar/gkp356. |
| Ion Mode: | NEGATIVE |
