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
Email	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

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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

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

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.

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