Summary of Study ST003072
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 PR001914. The data can be accessed directly via it's Project DOI: 10.21228/M89T5V 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 | ST003072 |
| Study Title | Investigation of polar metabolites by targeted LC-MS analysis from mouse adult or embryonic CSF and from adult serum. |
| Study Summary | To maximize discovery from samples with limited amounts, we optimized a method to detect the thyroid hormones ( 3,5,3’-L-triiodothyronine (T3) and 3,5,3’5’-L-tetraiodothyronine (T4)) as well as polar metabolites from central carbon metabolism from mouse adult or embryonic CSF and from adult mouse serum. Samples were ran on reverse phase and HILIC chromatography respectively. For polar metabolite analysis, we employed targeted metabolomics profiling of a panel of 200 compounds. We interrogated relative changes between fresh and frozen adult (male or female) CSF compared to fresh and frozen embryonic CSF. This data presents results from polar HILIC chromatography |
| Institute | Boston Childrens Hospital |
| Department | Pathology |
| Laboratory | Kanarek Lab |
| Last Name | Petrova |
| First Name | Boryana |
| Address | 300 Longwood Av |
| boryana.petrova@childrens.harvard.edu | |
| Phone | 617 |
| Submit Date | 2024-01-10 |
| Num Groups | 7 |
| Total Subjects | 19 |
| Num Males | 8 |
| Num Females | 6 |
| Study Comments | embryos also investigated. samples split for fresh and frozen conditions |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-02-14 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN005030 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Vanquish |
| Column | SeQuant ZIC- pHILIC (150 x 2.1mm,5um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap |
| Ion Mode | UNSPECIFIED |
| Units | a.u. |
MS:
| MS ID: | MS004769 |
| Analysis ID: | AN005030 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | MS Data Acquisition Conditions for Targeted Analysis of Polar Metabolites and Thyroid Hormones: MS data acquisition was performed using a Q Exactive Orbitrap benchtop orbitrap mass spectrometer equipped with an Ion Max source and a HESI II probe (Thermo Fisher Scientific, San Jose, CA, USA) in positive and negative ionization mode in a range of m/z = 70–1000, with the resolution set at 70,000, the AGC target at 1 × 106, and the maximum injection time (Max IT) at 20 msec. A narrower scan in positive mode at m/z = 600–800 was used for more specific detection of TH. The resolution was set at 70,000, the AGC target was 5 × 105, and the max IT was 100 msec. For polar metabolites, HESI conditions were as follows: sheath gas flow rate: 35 units; Aug gas flow rate: 8 units; sweet gas flow rate: 1 unit; spray voltage: 3.5 kV (pos), 2.8 kV (neg); capillary temperature: 320 °C; S-lens RF: 50; Aux gas heater temperature: 350 °C. For T3/T4, HESI conditions were as follows: sheath gas flow rate: 40 units; Aug gas flow rate: 10 units; sweet gas flow rate: 0; spray voltage: 3.5 kV (pos), 2.8 kV (neg); capillary temperature: 380 °C; S-lens RF: 60; Aux gas heater temperature: 420 °C. Targeted Metabolomics Data Analysis: Relative quantification of polar metabolites was performed with TraceFinder 5.1 (Thermo Fisher Scientific, Waltham, MA, USA) using a 5 ppm mass tolerance and referencing an in-house library of chemical standards (see associated Supplemental Dataset S1). We routinely queried 266 compounds (40 internal standards and 226 metabolites). Pooled samples and fractional dilutions were prepared as quality controls and injected at the beginning and end of each run. In addition, pooled samples were interspersed throughout the run to control for technical drift in signal quality as well as to serve to assess the coefficient of variability (CV) for each metabolite. Data from TraceFinder were further consolidated and normalized with an in-house R script, freely accessible at github (https://github.com/FrozenGas/KanarekLabTraceFinderRScripts/blob/main/MS_data_script_v2.4_20221018.R). Briefly, this script performs the following normalization and quality control steps: (1) extracts and combines the peak areas from TraceFinder output.csvs; (2) calculates and normalizes to an averaged factor from all mean-centered chromatographic peak areas of isotopically labeled amino acid and QReSS internal standards within each sample; (3) filters out low-quality metabolites based on user-inputted cut-offs calculated from pool reinjections and pool dilutions; (4) calculates and normalizes for biological material amounts based on the total integrated peak area values of high-confidence metabolites. In this study, the linear correlation between the dilution factor and the peak area cut-offs is set to RSQ > 0.95 and the coefficient of variation (CV) < 30%. Finally, data were log transformed and Pareto scaled within the MetaboAnalyst-based statistical analysis platform [42] to generate PCA, PLSDA, volcano plots, and heatmaps. Individual metabolite bar plots and statistics were calculated in Excel (v16.81) and GraphPad Prism (v.10). |
| Ion Mode: | UNSPECIFIED |
