Summary of Study ST001974

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR001255. The data can be accessed directly via it's Project DOI: 10.21228/M8GT41 This work is supported by NIH grant, U2C- DK119886.


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.

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Study IDST001974
Study TitleAnti-oxidative metabolism measurement in mammalian cells and tissues by quantitative LC/MS method (I)
Study SummaryAnti-oxidative metabolism measurement in CSF of mice by quantitative LC/MS method to analyze effect of MTX on level of antioxidants in mouse controls 0-48hrs in CSF and hippocampus.
Boston Children's Hospital, Harvard Medical School
Last NamePetrova
First NameBoryana
Address300 Longwood Ave
Submit Date2021-09-04
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2022-08-29
Release Version1
Boryana Petrova Boryana Petrova application/zip

Select appropriate tab below to view additional metadata details:


Project ID:PR001255
Project DOI:doi: 10.21228/M8GT41
Project Title:Gene-therapy enhances CSF’s anti-oxidative activity to mitigate chemotherapy side effects
Project Type:Anti-oxidative Metabolism Measurement in CSF of MTX-treated mice under gene therapy by quantitative LC/MS method
Project Summary:In order to test the protective activity of SOD3 levels on the redox state of the CSF of MTX-treated mice, targeted metabolomics on CSF was employed at different timepoints after treatment, on mice of both sexes, at various levels of impacted hSOD3 expression.
Institute:Boston Childrens Hospital
Laboratory:Naama Kanarek
Last Name:Petrova
First Name:Boryana
Address:300 Longwood Av, Boston, MA, 2115, USA


Subject ID:SU002054
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Gender:Male and female


Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Factor
SA185254pooled sample QCd-
SA185255pooled sample QCc-
SA185256pooled sample QCa-
SA185257pooled sample Qce-
SA185258pooled sample QCb-
SA185259pooled sample QC 1/3 dilution-
SA185260blank start-
SA185261pooled sample QC 1/10 dilution b-
SA185262blank end-
SA185263pooled sample QC 1/10 dilution a-
SA185264mouse CSF 20female 24h
SA185265mouse CSF 22female 24h
SA185266mouse CSF 19female 24h
SA185267mouse CSF 21female 24h
SA185268mouse CSF 29female 48h
SA185269mouse CSF 30female 48h
SA185270mouse CSF 27female 48h
SA185271mouse CSF 28female 48h
SA185272mouse CSF 12female 4h
SA185273mouse CSF 13female 4h
SA185274mouse CSF 14female 4h
SA185275mouse CSF 11female 4h
SA185276mouse CSF 5female ctl
SA185277mouse CSF 6female ctl
SA185278mouse CSF 4female ctl
SA185279mouse CSF 18male 24h
SA185280mouse CSF 17male 24h
SA185281mouse CSF 16male 24h
SA185282mouse CSF 15male 24h
SA185283mouse CSF 24male 48h
SA185284mouse CSF 23male 48h
SA185285mouse CSF 25male 48h
SA185286mouse CSF 26male 48h
SA185287mouse CSF 7male 4h
SA185288mouse CSF 8male 4h
SA185289mouse CSF 9male 4h
SA185290mouse CSF 10male 4h
SA185291mouse CSF 2male ctl
SA185292mouse CSF 1male ctl
SA185293mouse CSF 3male ctl
Showing results 1 to 40 of 40


Collection ID:CO002047
Collection Summary:All animal studies were performed under the protocol approved by the Institutional Animal Care and Use Committee (IACUC) of Boston Children’s Hospital (BCH). CD-1 mice (timed pregnant and 6-8 weeks) and Sprague Dawley rats (6-8 weeks) were purchased (Charles River Laboratories). Male and female animals were used equally for all studies. All animals were housed in a 12h light-dark cycle with ad libitum access to food and water. CSF was collected from the cisterna magna and centrifuged at 10,000g for 10 min. at 4 °C to remove any tissue debris (38). CSF samples were flash frozen and stored at −80°C until use.
Sample Type:CSF


Treatment ID:TR002066
Treatment Summary:Control CSF + buffers from Study Design

Sample Preparation:

Sampleprep ID:SP002060
Sampleprep Summary:For characterization by mass spectrometry, CSF was acquired 4h, 24h, and 48h following a single 75 mg/kg MTX injection from 6-8 mice and flash frozen for further analysis. Per condition, 3 μl of CSF were extracted by brief sonication in 240 μl 100% methanol, supplemented with isotopically labeled internal standards (17 amino acids and reduced glutathione, Cambridge Isotope Laboratories, MSK-A2-1.2 and CNLM-6245-10) and 60 μl 20 mM Ellman’s reagent in water (Sigma-Aldrich, D8130). After centrifugation for 10min. at maximum speed on a benchtop centrifuge (Eppendorf) the cleared supernatant was dried using a nitrogen dryer and reconstituted in 30 µl water by brief sonication. Extracted metabolites were spun again and cleared supernatant was transferred in LC-MS microvials. A small amount of each sample was pooled and serially diluted 3 and 10-fold to be used as quality controls throughout the batch run. Two microliters (equivalent to 0.2 ul of CSF) of reconstituted sample were injected into a ZIC-pHILIC 150 × 2.1 mm (5 µm particle size) column (EMD Millipore) operated on a Dionex UltiMate 3000 UPLC system (Thermo Fisher Scientific). Chromatographic separation was achieved using the following conditions: buffer A was acetonitrile; buffer B was 20 mM ammonium carbonate, 0.1% ammonium hydroxide. Gradient conditions were: linear gradient from 20% to 80% B; 20–20.5 min: from 80% to 20% B; 20.5–28 min: hold at 20% B. The column oven and autosampler tray were held at 25 °C and 4 °C, respectively. The MS data acquisition was on a QExactive benchtop orbitrap mass spectrometer equipped with an Ion Max source and a HESI II probe and was performed in a range of m/z= 70–1000, with the resolution set at 70,000, the AGC target at 1x106, and the maximum injection time (Max IT) at 20 msec. For tSIM scans, the resolution was set at 70,000, the AGC target was 1x105, and the max IT was 100 msec. Relative quantitation of polar metabolites was performed with TraceFinder 4.1 (Thermo Fisher Scientific) using a 5 ppm mass tolerance and referencing an in-house library of chemical standards. Pooled samples and fractional dilutions were prepared as quality controls and only those metabolites were taken for further analysis, for which the correlation between the dilution factor and the peak area was >0.95 (high confidence metabolites). Normalization for biological material amounts was based on the total integrated peak area values of high-confidence metabolites within an experimental batch after normalizing to the averaged factor from all mean-centered chromatographic peak areas of isotopically labeled amino acids internal standards (Cambridge Isotope Laboratories). The data were Log transformed and Pareto scaled for MetaboAnalyst-based statistical or pathway analysis (41). We profiled 200 metabolites, 85 of which were detected in CSF and passed our quality control protocol.

Combined analysis:

Analysis ID AN003222
Analysis type MS
Chromatography type HILIC
Chromatography system Thermo Q Exactive Orbitrap
Column EMD Millipore ZIC-HILIC (100 x 2.1mm,3.5um)
MS instrument type Orbitrap
MS instrument name Thermo Exactive Plus Orbitrap
Units ppm


Chromatography ID:CH002376
Instrument Name:Thermo Q Exactive Orbitrap
Column Name:EMD Millipore ZIC-HILIC (100 x 2.1mm,3.5um)
Chromatography Type:HILIC


MS ID:MS002996
Analysis ID:AN003222
Instrument Name:Thermo Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Comments:Xcalibur + Tracefinder