Summary of Study ST001952
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 PR001239. The data can be accessed directly via it's Project DOI: 10.21228/M8JT51 This work is supported by NIH grant, U2C- DK119886.
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Study ID | ST001952 |
Study Title | GLS2KO vs WT mouse hepatocytes |
Study Type | Genotype |
Study Summary | Test the effect of GLS2 knockout in primary mouse hepatocytes. We isolated hepatocytes from GLS2 knockout and wild-type mice, and briefly applied media lacking L-glutamine (2 hours). Sixty minutes after resupplying Gln, metabolites were extracted and analyzed with the Mixed Mode method. Data were processed through XCMS, and features were filtered for p<0.01, fold change >2, and a minimum intensity of 1x10^6. Sorting by smallest p value, the first extracted ion chromatogram (EIC) with good chromatographic peak shape corresponded to 188.0567m/z at 24.41 min. Six putative IDs were within 3ppm of the experimentally observed m/z, representing two chemical formulas, none of which had documented retention times in training or test sets. Amongst these potential IDs, the Message Passing Neural Network (MPNN) model correctly predicted N-acetyl-L-glutamic acid as the most likely candidate, as verified by injection of purchased standards. The next most significant difference between GLS2KO vs WT was 117.0196m/z observed at 20.07 minutes. The model had been trained on 2/6 of the putative IDs. Despite the four additional isomers suggested, the model correctly selected succinate as reduced by GLS2 KO (Figure 5B). The third most significant hit corresponds to 171.0068m/z at 23.11 min. Although glycerol 1-P and 2-P are both potential hits, almost indistinguishable by the model, the large gap in retention times between these top hits and the Cl- adducts of threonate (+ isomers) is apparent, further supporting the correct identification as glycerol mono-phosphate. Expansion of the list to include p<0.05 leads to the identification of Glutamine, Glutamate, and other downstream metabolites known to be altered by GLS2 KO. |
Institute | Pfizer |
Last Name | Clasquin |
First Name | Michelle |
Address | 1 Portland St., Cambridge, MA 02139 |
michelle.clasquin@pfizer.com | |
Phone | 6174487289 |
Submit Date | 2021-10-22 |
Num Groups | 2 |
Total Subjects | 6 |
Num Males | 6 |
Raw Data Available | Yes |
Raw Data File Type(s) | mzXML |
Analysis Type Detail | LC-MS |
Release Date | 2021-11-08 |
Release Version | 1 |
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Combined analysis:
Analysis ID | AN003177 |
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Analysis type | MS |
Chromatography type | Unspecified |
Chromatography system | Dionex UltiMate 3000 RSLC |
Column | HILICpak VT50 2D (150 mm x 2.0 mm,5um particle size,Shodex,Japan) |
MS Type | ESI |
MS instrument type | Orbitrap |
MS instrument name | Thermo Q Exactive Plus Orbitrap |
Ion Mode | NEGATIVE |
Units | Peak area |
Chromatography:
Chromatography ID: | CH002349 |
Chromatography Summary: | Liquid chromatography separation was achieved on a HILICpak VT50 2D column (150 mm x 2.0 mm, 5 µm particle size, Shodex, Japan). Buffer A consists of 90% acetonitrile, 10% water, containing 20 mM Triethylamine : Formic acid at pH 9.18; Buffer B consists of 5% acetonitrile, 95% water containing 54 mM Triethyl-amine : Formic acid at pH 3.03. Flow rate is 0.2mL/min from 0 to 5 minutes, then 0.3 mL/min from 5.1 to 58 min, and reduced again to 0.2mL/min from 58.1 to 60 min. The gradient starts with 0%B from 0 to 10 min, then increases linearly from 0 to 16%B from 10 to 27 min, up to 65%B at 32 min, 87%B at 34 min, 100%B hold from 34.1 to 47 min, then 0%B from 47.1 to 60 min. |
Instrument Name: | Dionex UltiMate 3000 RSLC |
Column Name: | HILICpak VT50 2D (150 mm x 2.0 mm,5um particle size,Shodex,Japan) |
Chromatography Type: | Unspecified |