Summary of Study ST001186
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 PR000798. The data can be accessed directly via it's Project DOI: 10.21228/M8J399 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 | ST001186 |
| Study Title | Untargeted metabolomics on control and compound-treated STHdhQ111 cells and control STHdhQ7 cells |
| Study Summary | Cells expressing mutant huntingtin were treated in triplicate with serum-free DMEM with vehicle (Q111SST) or serum-free DMEM with one of 14 protective compounds for 24 hours. Wild type cells were also treated with serum-free DMEM with vehicle (Q7SST) as an additional control for 24 hours. We examined the compounds' metabolomic effects on the cells using untargeted mass spectrometry, which measured lipids and polar metabolites. |
| Institute | Massachusetts Institute of Technology |
| Laboratory | Fraenkel Lab |
| Last Name | Patel-Murray |
| First Name | Natasha |
| Address | 77 Massachusetts Avenue, Building 16 Room 244 |
| nlpm@mit.edu | |
| Phone | 6179490941 |
| Submit Date | 2019-05-24 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2020-01-22 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN001975 | AN001976 | AN001977 | AN001978 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | HILIC | HILIC |
| Chromatography system | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 |
| Column | Ascentis Express C18 (150 x 2.1mm,2.7um) | Ascentis Express C18 (150 x 2.1mm,2.7um) | EMD Millipore ZIC-HILIC (100 x 2.1mm,3.5um) | EMD Millipore ZIC-HILIC (100 x 2.1mm,3.5um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE | POSITIVE | NEGATIVE |
| Units | Peak area | Peak area | Peak Area | Peak Area |
MS:
| MS ID: | MS001829 |
| Analysis ID: | AN001975 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | For lipid profiling, cells were resuspended in 50uL 60/35/5 acetonitrile/isopropanol/water (v/v/v) and 5uL was injected for LC/MS analysis. Please see Keckesova et al. and Smulan et al. for a detailed description of the LC/MS analysis (Smulan et al, 2016; Keckesova et al, 2017). Lipid identification and relative quantification was performed using LipidSearch (ThermoFisher Scientific / Mitsui Knowledge Industries). The identified lipids were subjected to quality control filtering and normalization by total signal (Keckesova et al, 2017). |
| Ion Mode: | POSITIVE |
| MS ID: | MS001830 |
| Analysis ID: | AN001976 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | For lipid profiling, cells were resuspended in 50uL 60/35/5 acetonitrile/isopropanol/water (v/v/v) and 5uL was injected for LC/MS analysis. Please see Keckesova et al. and Smulan et al. for a detailed description of the LC/MS analysis (Smulan et al, 2016; Keckesova et al, 2017). Lipid identification and relative quantification was performed using LipidSearch (ThermoFisher Scientific / Mitsui Knowledge Industries). The identified lipids were subjected to quality control filtering and normalization by total signal (Keckesova et al, 2017). |
| Ion Mode: | NEGATIVE |
| MS ID: | MS001831 |
| Analysis ID: | AN001977 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | For polar metabolite profiling, cells were resuspended in 100uL water and 2uL was injected for LC/MS analysis. Please see Birsoy et al. and Chen at al. for a detailed description of the LC/MS analysis (Chen et al, 2016; Birsoy et al, 2015). Untargeted analysis was performed using Progenesis CoMet (Nonlinear Dynamics) using the default settings. Features were filtered based on replicate injections and a dilution series of a pooled sample prepared by mixing equal aliquots of the biological samples. Specifically, the filtering criteria were CV < 0.4 across the four replicate injections and R > 0.9 across a four-point dilution series (comprising 0.1X, 0.3X and 1X concentrations, and a double-volume injection). Features that were not lowest according to the Progenesis quantification in the blank water injection samples were discarded. |
| Ion Mode: | POSITIVE |
| MS ID: | MS001832 |
| Analysis ID: | AN001978 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | For polar metabolite profiling, cells were resuspended in 100uL water and 2uL was injected for LC/MS analysis. Please see Birsoy et al. and Chen at al. for a detailed description of the LC/MS analysis (Chen et al, 2016; Birsoy et al, 2015). Untargeted analysis was performed using Progenesis CoMet (Nonlinear Dynamics) using the default settings. Features were filtered based on replicate injections and a dilution series of a pooled sample prepared by mixing equal aliquots of the biological samples. Specifically, the filtering criteria were CV < 0.4 across the four replicate injections and R > 0.9 across a four-point dilution series (comprising 0.1X, 0.3X and 1X concentrations, and a double-volume injection). Features that were not lowest according to the Progenesis quantification in the blank water injection samples were discarded. |
| Ion Mode: | NEGATIVE |
