Summary of Study ST001037
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 PR000694. The data can be accessed directly via it's Project DOI: 10.21228/M8ZT2M This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST001037 |
| Study Title | High Resolution GC-MS and FID Metabolomics of Human Serum |
| Study Type | Human Serum Analysis |
| Study Summary | We explored the possibility of performing quantitative metabolomics using a QEGC-MS using both FID and MS detectors as complementary techniques. |
| Institute | Wake Forest Baptist Medical Center |
| Department | Center for Precision Medicine |
| Laboratory | Michael Olivier Laboratory |
| Last Name | Misra |
| First Name | Biswapriya |
| Address | Medical Center Boulevard NRC Building, G#43, Medical Center Boulevard, Winston Salem, NC, 27157, USA |
| bbmisraccb@gmail.com | |
| Phone | 3522156040 |
| Submit Date | 2018-08-13 |
| Total Subjects | 1 |
| Num Males | 1 |
| Study Comments | NA |
| Publications | In process |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | GC-MS |
| Release Date | 2019-01-22 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000694 |
| Project DOI: | doi: 10.21228/M8ZT2M |
| Project Title: | High Resolution GC-MS and FID Metabolomics of Human Serum |
| Project Type: | Method Development in Metabolomics |
| Project Summary: | We explored the combination of MS and FID detector as dual approach to obtain quantitative metabolomics data on a QE-GC-Orbitrap-MS platform. |
| Institute: | Wake Forest Baptist Medical Center |
| Department: | Center for Precision Medicine |
| Laboratory: | Michael Olivier Laboratory |
| Last Name: | Misra |
| First Name: | Biswapriya |
| Address: | Medical Center Boulevard NRC Building, G#43, Medical Center Boulevard, Winston Salem, NC, 27157, USA |
| Email: | bbmisraccb@gmail.com |
| Phone: | 3522156040 |
| Funding Source: | NA |
| Project Comments: | NA |
| Publications: | In process |
| Contributors: | Biswapriya B. Misra, Ekong Bassey, Michael Olivier |
Subject:
| Subject ID: | SU001076 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Genotype Strain: | NA |
| Age Or Age Range: | NA |
| Gender: | Male |
| Human Race: | NA |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Description |
|---|---|---|
| SA069382 | B1 | Blank |
| SA069383 | B3 | Blank |
| SA069384 | B2 | Blank |
| SA069385 | R3 | Reagent Blank |
| SA069386 | R1 | Reagent Blank |
| SA069387 | R2 | Reagent Blank |
| SA069388 | S5_3 | Serum Sample |
| SA069389 | S4_1 | Serum Sample |
| SA069390 | S3_3 | Serum Sample |
| SA069391 | S4_2 | Serum Sample |
| SA069392 | S4_3 | Serum Sample |
| SA069393 | S5_2 | Serum Sample |
| SA069394 | S5_1 | Serum Sample |
| SA069395 | S3_2 | Serum Sample |
| SA069396 | S2_1 | Serum Sample |
| SA069397 | S3_1 | Serum Sample |
| SA069398 | S1_1 | Serum Sample |
| SA069399 | S1_3 | Serum Sample |
| SA069400 | S1_2 | Serum Sample |
| SA069401 | S2_2 | Serum Sample |
| SA069402 | S2_3 | Serum Sample |
| SA069403 | P1 | Solvent |
| SA069404 | P3 | Solvent |
| SA069405 | P2 | Solvent |
| Showing results 1 to 24 of 24 |
Collection:
| Collection ID: | CO001070 |
| Collection Summary: | Purchased Serum from Sigma Aldrich. |
| Sample Type: | Human Serum from Commercial Source |
| Collection Method: | NA |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001090 |
| Treatment Summary: | None. |
Sample Preparation:
| Sampleprep ID: | SP001083 |
| Sampleprep Summary: | Serum samples (30 µL) were subjected to sequential solvent extraction once each with 1 mL of acetonitrile: isopropanol: water (3:3:2, v/v) ratio and 500 µL of acetonitrile: water (1:1, v/v) ratio mixtures at 4 C.22 Adonitol and d4-succinic acid (both 5 µL from 10 mg/ml stock) were added to each aliquots as two internal standards prior to the extraction. The pooled extracts (~ 1500 µL) from the two steps were dried under vacuum at 4 C prior to chemical derivatization. Dummy extractions performed on blank tubes served as extraction blanks to account for background (extraction solvent, derivatization reagents) noise and other sources of contamination (septa, liner, column, vials, handling etc.). Blanks were only used to see that no carry overs occurred during randomized run orders and to manually filter out contaminating chemicals from the combined list of features. Samples were then sequentially derivatized with methoxyamine hydrochloride (MeOX) and 1% TMCS in N-methyl-N-trimethylsilyl-trifluoroacetamide (MSTFA) as described elsewhere.23,24 Steps involved addition of 10 μL of MeOX (20 mg/mL) in pyridine incubated under shaking at 55 °C for 60 min followed by trimethylsilylation at 60 °C for 60 min after adding 90 μL MSTFA. |
| Sampleprep Protocol ID: | Fiehn et al., 2008 |
| Sampleprep Protocol Comments: | NA |
| Processing Method: | Fiehn et al., 2008 |
| Processing Storage Conditions: | On ice |
| Extraction Method: | Fiehn et al., 2008 |
| Extract Enrichment: | None |
| Extract Cleanup: | None |
| Sample Resuspension: | NA |
| Sample Derivatization: | Methoxyaminatin + silylation (MSTFA) |
| Sample Spiking: | Adonitol |
| Subcellular Location: | NA |
Combined analysis:
| Analysis ID | AN001698 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | QEOrbitrap-GC-MS |
| Column | TraceGOLD TG-5SILMS |
| MS Type | EI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE |
| Units | Abundance |
Chromatography:
| Chromatography ID: | CH001197 |
| Chromatography Summary: | A robotic arm TriPlus™ RSH autosampler (Thermo Scientific™, Bremen, Germany) injected 1µL of derivatized sample into a split/splitless (SSL) injector at 250 °C using a 1:100 split flow on TRACE™ 1310 gas chromatograph (Thermo Scientific™, Austin, TX). Helium carrier gas at a flow rate of 1 mL/min was used for separation on a Thermo Scientific™ TraceGOLD™ TG-5SILMS 30 m length × 0.25 mm i.d. × 0.25 µm film thickness column. The initial oven temperature was held at 70 °C for 4 min, followed by an initial gradient of 20 °C/min ramp rate. The final temperature was 320 °C and held for 8 min. |
| Instrument Name: | QEOrbitrap-GC-MS |
| Column Name: | TraceGOLD TG-5SILMS |
| Chromatography Type: | GC |
MS:
| MS ID: | MS001573 |
| Analysis ID: | AN001698 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | EI |
| Ion Mode: | POSITIVE |
| Fragmentation Method: | EI |
| Helium Flow: | 1 ml/min |
| Ion Source Temperature: | 250 |
