Summary of Study ST001979

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 IDST001979
Study TitleAnti-oxidation metabolism measurement in mammalian cells and tissues by quantitative LC/MS method (VI)
Study SummaryAnti-oxidation metabolism measurement in mouse CSF by quantitative LC/MS method.
Boston Children's Hospital, Harvard Medical School
Last NamePetrova
First NameBoryana
Address300 Longwood Ave
Submit Date2021-09-15
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:SU002059
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
SA185499pooled sample QC 1f-
SA185500pooled sample QC 1g-
SA185501pooled sample QC 1h-
SA185502pooled sample QC 1e-
SA185503pooled sample QC 1d-
SA185504pooled sample QC 1b-
SA185505pooled sample QC 1c-
SA185506pooled sample QC 1/3 dilution-
SA185507pooled sample QC 1/10 dilution a-2x-
SA185508blank 3-
SA185509blank 4-
SA185510blank 2-
SA185511blank 1-
SA185512pooled sample QC 1/10 dilution a-
SA185513pooled sample QC 1/10 dilution b-
SA185514pooled sample QC 1a-
SA185524Mouse CSF Ctrl 49CMV-GFP-1
SA185525Mouse CSF Ctrl 50CMV-GFP-2
SA185526Mouse CSF Ctrl 51CMV-GFP-3
SA185527Mouse CSF Ctrl 52CMV-GFP-4
SA185528Mouse CSF Ctrl 53CMV-GFP-5
SA185529Mouse CSF Ctrl 54CMV-GFP-6
SA185515Mouse CSF Ctrl 55CMV-GFP+MTX-1
SA185516Mouse CSF Ctrl 56CMV-GFP+MTX-2
SA185517Mouse CSF Ctrl 57CMV-GFP+MTX-3
SA185518Mouse CSF Ctrl 58CMV-GFP+MTX-4
SA185519Mouse CSF Ctrl 59CMV-GFP+MTX-5
SA185520Mouse CSF Ctrl 60CMV-GFP+MTX-6
SA185521Mouse CSF Ctrl 61CMV-GFP+MTX-7
SA185522Mouse CSF Ctrl 62CMV-GFP+MTX-8
SA185523Mouse CSF Ctrl 63CMV-GFP+MTX-9
SA185539Mouse CSF Ctrl 1PBS-1
SA185540Mouse CSF Ctrl 2PBS-2
SA185541Mouse CSF Ctrl 3PBS-3
SA185542Mouse CSF Ctrl 4PBS-4
SA185543Mouse CSF Ctrl 5PBS-5
SA185544Mouse CSF Ctrl 6PBS-6
SA185545Mouse CSF Ctrl 7PBS-7
SA185546Mouse CSF Ctrl 8PBS-8
SA185547Mouse CSF Ctrl 9PBS-9
SA185530Mouse CSF Ctrl 10PBS+MTX-1
SA185531Mouse CSF Ctrl 11PBS+MTX-2
SA185532Mouse CSF Ctrl 12PBS+MTX-3
SA185533Mouse CSF Ctrl 13PBS+MTX-4
SA185534Mouse CSF Ctrl 14PBS+MTX-5
SA185535Mouse CSF Ctrl 15PBS+MTX-6
SA185536Mouse CSF Ctrl 16PBS+MTX-7
SA185537Mouse CSF Ctrl 17PBS+MTX-8
SA185538Mouse CSF Ctrl 18PBS+MTX-9
Showing results 1 to 49 of 49


Collection ID:CO002052
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:TR002071
Treatment Summary:Mice were treated with PBS, PBS+ MTX, Null GFP with and without MTX, CAG-GFP with and without MTX, and CMV-GFP with and without MTX. buffers from study design were used for all respective samples. CD-1 mice (6-8 weeks) or Sprague Dawley rats (8 weeks) were given a single intravenous injection of 75 mg/kg MTX (Fisher Scientific, AAJ66364MD) dissolved in 0.9 % NaCl (Mountainside Medical, 0409-4888-10). MTX was freshly prepared for each experiment. MTX in mouse serum or CSF was assessed by MTX ELISA according to the manufacturer's instructions (Enzo Life Sciences, 142-0001).

Sample Preparation:

Sampleprep ID:SP002065
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 AN003228 AN003229
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Column EMD Millipore ZIC-HILIC (100 x 2.1mm,3.5um) EMD Millipore ZIC-HILIC (100 x 2.1mm,3.5um)
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Exactive Plus Orbitrap Thermo Exactive Plus Orbitrap
Units ppm ppm


Chromatography ID:CH002381
Instrument Name:Thermo Q Exactive Orbitrap
Column Name:EMD Millipore ZIC-HILIC (100 x 2.1mm,3.5um)
Chromatography Type:HILIC


MS ID:MS003002
Analysis ID:AN003228
Instrument Name:Thermo Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Comments:Xcalibur + Tracefinder
MS ID:MS003003
Analysis ID:AN003229
Instrument Name:Thermo Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Comments:Xcalibur + Tracefinder