Summary of Study ST001978
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 PR001255. The data can be accessed directly via it's Project DOI: 10.21228/M8GT41 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
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.
Study ID | ST001978 |
Study Title | Anti-oxidation metabolism measurement in mammalian cells and tissues by quantitative LC/MS method (V) |
Study Summary | Anti-oxidation metabolism measurement in human patient CSF by quantitative LC/MS method. |
Institute | Boston Children's Hospital, Harvard Medical School |
Last Name | Petrova |
First Name | Boryana |
Address | 300 Longwood Ave |
boryana.petrova@childrens.harvard.edu | |
Phone | 6173557433 |
Submit Date | 2021-09-15 |
Raw Data Available | Yes |
Raw Data File Type(s) | raw(Thermo) |
Analysis Type Detail | LC-MS |
Release Date | 2022-08-29 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
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 |
Department: | Pathology |
Laboratory: | Naama Kanarek |
Last Name: | Petrova |
First Name: | Boryana |
Address: | 300 Longwood Av, Boston, MA, 2115, USA |
Email: | boryana.petrova@childrens.harvard.edu |
Phone: | 6173557433 |
Subject:
Subject ID: | SU002058 |
Subject Type: | Mammal |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Gender: | Male and female |
Factors:
Subject type: Mammal; Subject species: Homo sapiens (Factor headings shown in green)
mb_sample_id | local_sample_id | Factor |
---|---|---|
SA185419 | pooled sample QCc | - |
SA185420 | pooled sample QCd | - |
SA185421 | pooled sample QCb | - |
SA185422 | pooled sample QCa | - |
SA185423 | pooled sample QC 1b | - |
SA185424 | pooled sample QC 1/3 dilution | - |
SA185425 | pooled sample QC 1/10 dilution b | - |
SA185426 | blank 3 | - |
SA185427 | blank 4 | - |
SA185428 | blank 2 | - |
SA185429 | blank 1 | - |
SA185430 | pooled sample QC 1c | - |
SA185431 | pooled sample QC 1/10 dilution a | - |
SA185432 | pooled sample QC 1a | - |
SA185433 | blank 1-2 | - |
SA185434 | blank 1-1 | - |
SA185435 | pooled sample QC 1/10 dilution 1b | - |
SA185436 | blank 1-3 | - |
SA185437 | blank 1-4 | - |
SA185438 | blank 5 | - |
SA185439 | blank 1-6 | - |
SA185440 | blank 1-5 | - |
SA185441 | pooled sample QC 1/10 dilution 1a | - |
SA185442 | pooled sample QC 1/3 dilution 1a | - |
SA185443 | pooled sample QC 1d | - |
SA185444 | pooled sample QC 1e | - |
SA185445 | pooled sample QC 1e-1 | - |
SA185451 | human CSF 51 | L10-1 |
SA185452 | human CSF 52 | L10-2 |
SA185446 | human CSF 25 | L1-1 |
SA185447 | human CSF 26 | L1-2 |
SA185448 | human CSF 27 | L1-3 |
SA185449 | human CSF 28 | L1-4 |
SA185450 | human CSF 29 | L1-5 |
SA185453 | human CSF 30 | L2-1 |
SA185454 | human CSF 31 | L2-2 |
SA185455 | human CSF 32 | L3-1 |
SA185456 | human CSF 33 | L3-2 |
SA185457 | human CSF 34 | L3-3 |
SA185458 | human CSF 35 | L3-4 |
SA185459 | human CSF 36 | L3-5 |
SA185460 | human CSF 37 | L4-1 |
SA185461 | human CSF 38 | L4-2 |
SA185462 | human CSF 39 | L5-1 |
SA185463 | human CSF 40 | L5-2 |
SA185464 | human CSF 41 | L6-1 |
SA185465 | human CSF 42 | L6-2 |
SA185466 | human CSF 43 | L6-3 |
SA185467 | human CSF 44 | L7-1 |
SA185468 | human CSF 45 | L7-2 |
SA185469 | human CSF 46 | L8-1 |
SA185470 | human CSF 47 | L8-2 |
SA185471 | human CSF 48 | L9-1 |
SA185472 | human CSF 49 | L9-2 |
SA185473 | human CSF 50 | L9-3 |
SA185486 | mouse CSF 1 | mouse control |
SA185474 | human CSF 15 | N25 |
SA185475 | human CSF 16 | N55 |
SA185476 | human CSF 17 | N58 |
SA185477 | human CSF 18 | N61 |
SA185478 | human CSF 19 | N66 |
SA185479 | human CSF 20 | N75 |
SA185480 | human CSF 21 | N88 |
SA185481 | human CSF 1 | N9 |
SA185482 | human CSF 22 | N91 |
SA185483 | human CSF 23 | N93 |
SA185484 | human CSF 24 | N95 |
SA185485 | human CSF 2 | NJ3 |
SA185487 | human CSF 9 | patient12_1 12/5/02 |
SA185488 | human CSF 10 | patient12_2 1/16/03 |
SA185489 | human CSF 11 | patient12_3 5/23/03 |
SA185490 | human CSF 12 | patient13_1 12/29/11 |
SA185491 | human CSF 13 | patient13_2 4/28/14 |
SA185492 | human CSF 14 | patient13_3 7/16/14 |
SA185493 | human CSF 3 | patient2_1 6/10/07 |
SA185494 | human CSF 4 | patient2_2 6/11/07 |
SA185495 | human CSF 5 | patient2_3 4/22/08 |
SA185496 | human CSF 6 | patient4_1 8/31/10 |
SA185497 | human CSF 7 | patient4_2 6/11/11 |
SA185498 | human CSF 8 | patient4_3 7/9/11 |
Showing results 1 to 80 of 80 |
Collection:
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:
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 Type | ESI | ESI |
MS instrument type | Orbitrap | Orbitrap |
MS instrument name | Thermo Exactive Plus Orbitrap | Thermo Exactive Plus Orbitrap |
Ion Mode | UNSPECIFIED | UNSPECIFIED |
Units | ppm | ppm |
Chromatography:
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:
MS ID: | MS003000 |
Analysis ID: | AN003226 |
Instrument Name: | Thermo Exactive Plus Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Xcalibur + Tracefinder |
Ion Mode: | UNSPECIFIED |
MS ID: | MS003001 |
Analysis ID: | AN003227 |
Instrument Name: | Thermo Exactive Plus Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Xcalibur + Tracefinder |
Ion Mode: | UNSPECIFIED |