Summary of Study ST001977

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 IDST001977
Study TitleAnti-oxidative metabolism measurement in mammalian cells and tissues by quantitative LC/MS method (IV)
Study SummaryAnti-oxidation metabolism measurement in mammalian cells and tissues by quantitative LC/MS method of human patient/lymphoma patient CSF.
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:SU002057
Subject Type:Mammal
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Male and female


Subject type: Mammal; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Factor
SA185384pooled sample QC 1/10 dilution a-
SA185385pooled sample QC 1/10 dilution b-
SA185386pooled sample QC 1/5 dilution-
SA185387pooled sample QCb-
SA185388pooled sample QCd-
SA185389pooled sample QC 1/3 dilution-
SA185390pooled sample QC 1a-
SA185391pooled sample QC 1/10 dilution 1a-
SA185392pooled sample QC 1/10 dilution 1b-
SA185393pooled sample QC 1/3 dilution 1a-
SA185394pooled sample QC 1c-
SA185395pooled sample QC 1b-
SA185396blank 8-
SA185397pooled sample QCa-
SA185398blank 8-1-
SA185399blank 10-
SA185400blank 9-
SA185401human CSF 18CSF2 10.03
SA185402human CSF 15CSF3 11.22
SA185403human CSF 20CSF4 11.27
SA185404human CSF 16CSF5 11.27
SA185382human CSF 17"lymphoma, patient 1"
SA185383human CSF 19"lymphoma, patient 2 2020.02.07"
SA185405human CSF 14N9
SA185406human CSF 13NJ3
SA185407human CSF 7patient12_1
SA185408human CSF 8patient12_2
SA185409human CSF 9patient12_3
SA185410human CSF 10patient13_1
SA185411human CSF 11patient13_2
SA185412human CSF 12patient13_3
SA185413human CSF 1patient2_1
SA185414human CSF 2patient2_2
SA185415human CSF 3patient2_3
SA185416human CSF 4patient4_1
SA185417human CSF 5patient4_2
SA185418human CSF 6patient4_3
Showing results 1 to 37 of 37


Collection ID:CO002050
Collection Summary:De-identified CSF samples from both central nervous system (CNS) lymphoma patients and non-chemotherapy exposed controls were obtained by Dr. Eric Wong (BIDMC) under BIDMC Institutional Review Board (IRB)-approved protocols and analyzed under BCH IRB-approved protocols. Samples were aliquoted and stored at −80°C until use. CSF from patient samples was collected independently and aliquoted in 3uL or 5uL amounts for analysis.
Sample Type:CSF


Treatment ID:TR002069
Treatment Summary:No treatment + buffers from study design

Sample Preparation:

Sampleprep ID:SP002063
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. Single-cell transcriptomics Mouse embryonic ChP single cell RNA-seq dataset was acquired and analyzed in (35). Briefly, whole embryonic ChP tissue from each ventricle was micro-dissected, digested, and live cells were FACS sorted. Single cells (~7,000 cells) were processed through the 10X Genomics Single Cell 3’ platform. Variable genes were selected by using the method described in (42). Briefly, a logistic regression model was fit to the cellular detection fraction as a function of total numbers of unique molecular identifiers (UMIs) per cell. Outliers from this curve (i.e., genes expressed in fewer cells than expected given the number of UMIs) were genes that contained more variance than proportionally expected, and therefore were particularly suited for reducing the dimensionality of the dataset. We used a threshold of deviance of -0.15 and determined the variable genes independently for each of three experimental replicates. The genes that were at the intersection of these three replicate gene lists (i.e., global variable genes) were used for downstream analysis. The expression matrix was restricted to the subset of these global variable genes, and then centered and scaled before performing principle component analysis (PCA) using Seurat’s RunPCA() function. After PCA, the number of significant principle components was determined to be 5 using the elbow method. The data were then visualized as a 2D embedding of the significant principle components using t-SNE (43) via the RunTSNE() function in Seurat.

Combined analysis:

Analysis ID AN003225
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:CH002379
Instrument Name:Thermo Q Exactive Orbitrap
Column Name:EMD Millipore ZIC-HILIC (100 x 2.1mm,3.5um)
Chromatography Type:HILIC


MS ID:MS002999
Analysis ID:AN003225
Instrument Name:Thermo Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Comments:Xcalibur + Tracefinder