Summary of Study ST001946
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 PR001233. The data can be accessed directly via it's Project DOI: 10.21228/M8B99H This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
Study ID | ST001946 |
Study Title | Bipolar disorder metabolomics analysis using FiehnLib and GMD for curation |
Study Type | Untargeted GC analysis |
Study Summary | In this study we analyzed the blood serum from 14 controls and 14 BD patients using GC-MS under the conditions required for the use of FiehnLib library with GMD as secondary library for curation on a untargeted metabolomics approach |
Institute | University of Campinas |
Department | Chemistry Institute, Department of Analytical Chemistry |
Laboratory | Laboratory of Bioanalytics and Integrated Omics (LaBIOmics) |
Last Name | Ribeiro |
First Name | Henrique |
Address | Rua Sérgio Buarque de Holanda,s/n |
hcarachoribeiro@gmail.com | |
Phone | +55 19 3521 3018 |
Submit Date | 2021-10-11 |
Num Groups | 2 |
Total Subjects | 28 |
Num Males | 11 |
Num Females | 17 |
Raw Data Available | Yes |
Raw Data File Type(s) | cdf |
Analysis Type Detail | GC-MS |
Release Date | 2021-11-04 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
Project ID: | PR001233 |
Project DOI: | doi: 10.21228/M8B99H |
Project Title: | Bipolar Disorder metabolomics analysis |
Project Type: | MS untargeted analysis |
Project Summary: | MS untargeted analysis using FiehnLib and GOLM metabolite database for data curation |
Institute: | University of Campinas |
Department: | Chemistry Institute, Department of Analytical Chemistry |
Laboratory: | Laboratory of Bioanalytics and Integrated Omics (LaBIOmics) |
Last Name: | Ribeiro |
First Name: | Henrique |
Address: | Rua Sérgio Buarque de Holanda,s/n |
Email: | hcarachoribeiro@gmail.com |
Phone: | +55 19 3521 3018 |
Funding Source: | CAPES |
Contributors: | Henrique Caracho Ribeiro, Alessandra Sussulini, Matej Oresic, Alex Dickens, Partho Sen |
Subject:
Subject ID: | SU002024 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Age Or Age Range: | 19-79 |
Weight Or Weight Range: | 49-93 |
Height Or Height Range: | 1.5-1.9 |
Gender: | Male and female |
Human Ethnicity: | Brazilian |
Human Medications: | BD patients used a wide range of different medications, mostly mood stabilizers and antipsychotics |
Human Inclusion Criteria: | Controls: Any adult over 18 years respecting the excusion criteria / BD: Any adult over 18 years old with BD diagnosed by a psychiatrist, respecting exclusion criteria psychiat |
Human Exclusion Criteria: | Controls : negative history of any psychiatric disorder or use of any kind of psychiatric medication / BD : concomitant diseases such as AIDS, hepatitis, endocrinal or metabolic diseases, substance use (except nicotine dependence), and pregnancy or postpartum period |
Species Group: | Mammals |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
mb_sample_id | local_sample_id | Condition |
---|---|---|
SA183503 | B14 | Bipolar |
SA183504 | B11 | Bipolar |
SA183505 | B15 | Bipolar |
SA183506 | B16 | Bipolar |
SA183507 | B01 | Bipolar |
SA183508 | B10 | Bipolar |
SA183509 | B12 | Bipolar |
SA183510 | B05 | Bipolar |
SA183511 | B09 | Bipolar |
SA183512 | B02 | Bipolar |
SA183513 | B06 | Bipolar |
SA183514 | B03 | Bipolar |
SA183515 | B07 | Bipolar |
SA183516 | B08 | Bipolar |
SA183517 | D11 | Control |
SA183518 | D10 | Control |
SA183519 | D12 | Control |
SA183520 | D14 | Control |
SA183521 | D09 | Control |
SA183522 | D13 | Control |
SA183523 | D01 | Control |
SA183524 | D03 | Control |
SA183525 | D02 | Control |
SA183526 | D04 | Control |
SA183527 | D05 | Control |
SA183528 | D07 | Control |
SA183529 | D06 | Control |
SA183530 | D08 | Control |
Showing results 1 to 28 of 28 |
Collection:
Collection ID: | CO002017 |
Collection Summary: | The blood was collected in a Vacutainer tube, left at ambient temperature for 30 minutes, and then stored on ice for the blood to coagulate. Afterward, the samples were centrifuged at 3500 g for 15 minutes at 4 °C. The blood serum was collected and transferred to microtubes, stored at -80 °C for further analysis. |
Sample Type: | Blood (serum) |
Storage Conditions: | -80℃ |
Treatment:
Treatment ID: | TR002036 |
Treatment Summary: | Samples were aliquoted into 100uL microtubes, and treated with sodium azide 0.01% (m/v), then stored in biofreezer at -80 °C until further analysis. |
Sample Preparation:
Sampleprep ID: | SP002030 |
Sampleprep Summary: | The metabolites from serum samples were extracted by a simple protein precipitation method, using 50 µL of serum and 150 µL of MeOH and 150 µL of pentadecanoic acid as the internal standard. The mixture was vortexed, centrifuged at 15000 RPM, subsequently separating and discarding the protein phase. The aqueous phase was then dried in a SpeedVac at room temp and the dried samples were then submitted to a two-step derivatization, where 10 µL of methoxamine hydrochloride pyridine solution (40 mg mL-1) was added to the sample, kept at 30 ºC for 90 minutes. After the first derivatization step, 90 µL of MSTFA with 1 % (v/v) of TMCS (trimethylchlorosilane) was added, with the sample being kept at 37 ºC for 30 minutes. |
Combined analysis:
Analysis ID | AN003168 |
---|---|
Analysis type | MS |
Chromatography type | GC |
Chromatography system | HP/Agilent 5890 Series II |
Column | HP5-MS (30m x 0.25mm x 0.25um) + Duragard precolumn (10m) |
MS Type | EI |
MS instrument type | Single quadrupole |
MS instrument name | HP 5970 Series Quadrupole Mass Selective Detector |
Ion Mode | UNSPECIFIED |
Units | Intensities after normalization by Internal standard and log2 transformed |
Chromatography:
Chromatography ID: | CH002341 |
Chromatography Summary: | The following GC/MS conditions were used. An HP 5890 Series II oven was ramped by 10°C/min from 60°C (1 min initial time) to 325°C (10 min final time), resulting in a 37.5 min run time with cooling down to 60°C. 10 µL was injected into the Agilent split/splitless injector at 250°C in splitless mode. A 30 m long HP5-MS column with 10 m Duragard precolumn was used with 0.25 mm diameter and 0.25 µm film thickness. A constant flow rate of 1 mL/min helium was used as carrier gas. The quadrupole mass spectrometer was switched on after a 5.90 min solvent delay time, scanning from 50-600 u. The source temperature was set to 230°C and the quadrupole temperature was 150°C. |
Instrument Name: | HP/Agilent 5890 Series II |
Column Name: | HP5-MS (30m x 0.25mm x 0.25um) + Duragard precolumn (10m) |
Chromatography Type: | GC |
MS:
MS ID: | MS002946 |
Analysis ID: | AN003168 |
Instrument Name: | HP 5970 Series Quadrupole Mass Selective Detector |
Instrument Type: | Single quadrupole |
MS Type: | EI |
MS Comments: | The GC-MS conditions were the same as required to use the FiehnLib library (Kind et al., 2009). The data obtained were exported as ‘.AIA’ format in GC Chemstation then transformed in ‘.d’ using Agilent GC-MS translator and finally converted in ‘.abf’ format using MS-DIAL ABF file converter. The ‘.abf’ files were then analyzed in MS-DIAL (version 4.16) for peak picking, deconvolution and peak identification. The peak table containing the identifications from FiehnLib and the respective intensities in total ion chromatogram (TIC) from each metabolite were exported and analyzed using R statistical programming language (version 3.60) to evaluate the relative standard deviations (RSD) from each metabolite on the QC samples. Metabolites with RSD > 30 % were discarded due to excessive deviation through the batch. We opted to perform a second curation of the identifications using Golm Metabolite Database (GMD) since was observed a deviation of ± 0.2 minutes on the identifications comparing to the value shown in the library, caused possibly by the equipment. Metabolites that presented inconsistencies between both platforms were considered unknown, where some of these were just identified by their functional groups using one of GMD functionalities. |
Ion Mode: | UNSPECIFIED |