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MB Sample ID: SA185480
Local Sample ID: | human CSF 21 |
Subject ID: | SU002058 |
Subject Type: | Mammal |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Gender: | Male and female |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU002058 |
Subject Type: | Mammal |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Gender: | Male and female |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
human CSF 21 | SA185480 | FL022873 | N88 | Factor |
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 |