Summary of Study ST001978

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 IDST001978
Study TitleAnti-oxidation metabolism measurement in mammalian cells and tissues by quantitative LC/MS method (V)
Study SummaryAnti-oxidation metabolism measurement in human patient 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 AvailableYes
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:SU002058
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
SA185419pooled sample QCc-
SA185420pooled sample QCd-
SA185421pooled sample QCb-
SA185422pooled sample QCa-
SA185423pooled sample QC 1b-
SA185424pooled sample QC 1/3 dilution-
SA185425pooled sample QC 1/10 dilution b-
SA185426blank 3-
SA185427blank 4-
SA185428blank 2-
SA185429blank 1-
SA185430pooled sample QC 1c-
SA185431pooled sample QC 1/10 dilution a-
SA185432pooled sample QC 1a-
SA185433blank 1-2-
SA185434blank 1-1-
SA185435pooled sample QC 1/10 dilution 1b-
SA185436blank 1-3-
SA185437blank 1-4-
SA185438blank 5-
SA185439blank 1-6-
SA185440blank 1-5-
SA185441pooled sample QC 1/10 dilution 1a-
SA185442pooled sample QC 1/3 dilution 1a-
SA185443pooled sample QC 1d-
SA185444pooled sample QC 1e-
SA185445pooled sample QC 1e-1-
SA185451human CSF 51L10-1
SA185452human CSF 52L10-2
SA185446human CSF 25L1-1
SA185447human CSF 26L1-2
SA185448human CSF 27L1-3
SA185449human CSF 28L1-4
SA185450human CSF 29L1-5
SA185453human CSF 30L2-1
SA185454human CSF 31L2-2
SA185455human CSF 32L3-1
SA185456human CSF 33L3-2
SA185457human CSF 34L3-3
SA185458human CSF 35L3-4
SA185459human CSF 36L3-5
SA185460human CSF 37L4-1
SA185461human CSF 38L4-2
SA185462human CSF 39L5-1
SA185463human CSF 40L5-2
SA185464human CSF 41L6-1
SA185465human CSF 42L6-2
SA185466human CSF 43L6-3
SA185467human CSF 44L7-1
SA185468human CSF 45L7-2
SA185469human CSF 46L8-1
SA185470human CSF 47L8-2
SA185471human CSF 48L9-1
SA185472human CSF 49L9-2
SA185473human CSF 50L9-3
SA185486mouse CSF 1mouse control
SA185474human CSF 15N25
SA185475human CSF 16N55
SA185476human CSF 17N58
SA185477human CSF 18N61
SA185478human CSF 19N66
SA185479human CSF 20N75
SA185480human CSF 21N88
SA185481human CSF 1N9
SA185482human CSF 22N91
SA185483human CSF 23N93
SA185484human CSF 24N95
SA185485human CSF 2NJ3
SA185487human CSF 9patient12_1 12/5/02
SA185488human CSF 10patient12_2 1/16/03
SA185489human CSF 11patient12_3 5/23/03
SA185490human CSF 12patient13_1 12/29/11
SA185491human CSF 13patient13_2 4/28/14
SA185492human CSF 14patient13_3 7/16/14
SA185493human CSF 3patient2_1 6/10/07
SA185494human CSF 4patient2_2 6/11/07
SA185495human CSF 5patient2_3 4/22/08
SA185496human CSF 6patient4_1 8/31/10
SA185497human CSF 7patient4_2 6/11/11
SA185498human CSF 8patient4_3 7/9/11
Showing results 1 to 80 of 80


Collection ID:CO002051
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.
Sample Type:CSF


Treatment ID:TR002070
Treatment Summary:No treatment + buffers from study design, patient IDs match protocol description.

Sample Preparation:

Sampleprep ID:SP002064
Sampleprep Summary:CSF 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 AN003226 AN003227
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:CH002380
Instrument Name:Thermo Q Exactive Orbitrap
Column Name:EMD Millipore ZIC-HILIC (100 x 2.1mm,3.5um)
Chromatography Type:HILIC


MS ID:MS003000
Analysis ID:AN003226
Instrument Name:Thermo Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Comments:Xcalibur + Tracefinder
MS ID:MS003001
Analysis ID:AN003227
Instrument Name:Thermo Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Comments:Xcalibur + Tracefinder