Summary of Study ST000411

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 PR000321. The data can be accessed directly via it's Project DOI: 10.21228/M8Q886 This work is supported by NIH grant, U2C- DK119886.

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Study ID	ST000411
Study Title	Smoking and urinary metabolomics
Study Summary	This metabolomics projects was to evaluate the differences between pooled urine from smokers and non-smokers from NIST.
Institute	University of North Carolina
Laboratory	Sumner Lab
Last Name	Sumner
First Name	Susan
Address	Eastern Regional Comprehensive Metabolomics Resource Core, UNC Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC, 28081
Email	susan_sumner @unc.edu
Phone	704-250-5066
Submit Date	2016-06-13
Raw Data Available	Yes
Raw Data File Type(s)	fid
Chear Study	Yes
Analysis Type Detail	NMR
Release Date	2024-12-31
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR000321
Project DOI:	doi: 10.21228/M8Q886
Project Title:	SRM Proficiency
Project Summary:	Pooled urine samples from smokers (NIST SRM 3672) and non-smokers (NIST SRM 3673) were provided by NIH.
Institute:	National Institutes of Health
Department:	CHEAR
Last Name:	Sumner
First Name:	Su
Address:	3040 E. Cornwallis Road
Email:	ssumner@rti.org
Phone:	919-541-7479

Subject:

Subject ID:	SU000432
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Species Group:	Mammals

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id	local_sample_id	Group
SA020175	N3673-1f	Non-Smoker
SA020176	N3673-1e1	Non-Smoker
SA020177	N3673-1d1	Non-Smoker
SA020178	N3673-1f1	Non-Smoker
SA020179	N3673-1g1	Non-Smoker
SA020180	N3673-1h1	Non-Smoker
SA020181	N3673-1h	Non-Smoker
SA020182	N3673-1d	Non-Smoker
SA020183	N3673-1g	Non-Smoker
SA020184	N3673-1e	Non-Smoker
SA020185	N3672-1f	Smoker
SA020186	N3672-1h1	Smoker
SA020187	N3672-1e	Smoker
SA020188	N3672-1d1	Smoker
SA020189	N3672-1f1	Smoker
SA020190	N3672-1e1	Smoker
SA020191	N3672-1g	Smoker
SA020192	N3672-1d	Smoker
SA020193	N3672-1h	Smoker
SA020194	N3672-1g1	Smoker
SA020195	TotalPool_5	Total Pool
SA020196	TotalPool_4	Total Pool
SA020197	TotalPool_2	Total Pool
SA020198	TotalPool_1	Total Pool
SA020199	TotalPool_3	Total Pool

Showing results 1 to 25 of 25

Showing results 1 to 25 of 25

Collection:

Collection ID:	CO000426
Collection Summary:	Pooled urine samples from smokers (NIST SRM 3672) and non-smokers (NIST SRM 3673) were provided by NIH.
Sample Type:	Urine

Treatment:

Treatment ID:	TR000446
Treatment Summary:	Pooled urine samples from smokers (NIST SRM 3672) and non-smokers (NIST SRM 3673) were provided by NIH.

Sample Preparation:

Sampleprep ID:	SP000439
Sampleprep Summary:	Vials of pooled urine (smoker and non-smoker) were shipped the NIH RTI-RCMRC on dry ice and immediately stored at -80 °C after being logged in for metabolomics analysis. Five 1 mL aliquots of each pool were taken for NMR analysis. A total of 10 study samples were thawed on ice for sample preparation. Two aliquots (400 μl) of thawed urine from each sample was mixed with 230 μl of 0.5 mM phosphate buffer (pH 7.5) and 70 uL of Chenomx ISTD solution. A total study pool was created by mixing 150 μl of urine from each sample. Additionally, two random QC pools were created. The tubes were vortexed for 2 min on a multi-tube vortexer. A 600 µl aliquot of the supernatant was transferred into pre-labeled 5 mm (7”) NMR tubes for data acquisition on a 700 MHz spectrometer. 1H NMR spectra of urine samples were acquired on a Bruker 700 MHz NMR spectrometer (located at North Carolina State University, Raleigh, NC, USA) using a 5 mm cryogenically cooled ATMA inverse probe and ambient temperature of 25 ℃. A 1D NOESY presaturation pulse sequence (noesypr1d, [recycle delay (RD)-90°-t1-90°-tm-90°-acquire free induction decay (FID) was used for data acquisition. For each sample 16 transients were collected into 65k data points using a spectral width of 12.02 ppm, 2 s relaxation delay, 100 ms mixing time, and an acquisition time of 3.89 s per FID. The water resonance was suppressed using resonance irradiation during the relaxation delay and mixing time. NMR spectra were processed using TopSpin 3.2 software (Bruker-Biospin, Germany). Spectra were zero filled, and Fourier transformed after exponential multiplication with line broadening factor of 0.5. Phase and baseline of the spectra were manually corrected for each spectrum. Spectra were referenced internally to the DSS-d6 signal. The quality of each NMR spectrum was assessed for the level of noise and alignment of identified markers. Spectra were assessed for missing data and underwent quality checks. NMR bins (0.7-9.50 ppm) were created excluding water and urea (4.25- 6.5 ppm) using intelligent bucket integration of 0.04 ppm bucket width with 50% looseness using ACD NMR Processor (ACD Labs Inc, Toronto, Canada). Integrals of each of the bins were normalized to total integral of each of the spectrum.

Sampleprep ID:

SP000439

Sampleprep Summary:

Vials of pooled urine (smoker and non-smoker) were shipped the NIH RTI-RCMRC on dry ice and immediately stored at -80 °C after being logged in for metabolomics analysis. Five 1 mL aliquots of each pool were taken for NMR analysis. A total of 10 study samples were thawed on ice for sample preparation. Two aliquots (400 μl) of thawed urine from each sample was mixed with 230 μl of 0.5 mM phosphate buffer (pH 7.5) and 70 uL of Chenomx ISTD solution. A total study pool was created by mixing 150 μl of urine from each sample. Additionally, two random QC pools were created. The tubes were vortexed for 2 min on a multi-tube vortexer. A 600 µl aliquot of the supernatant was transferred into pre-labeled 5 mm (7”) NMR tubes for data acquisition on a 700 MHz spectrometer. 1H NMR spectra of urine samples were acquired on a Bruker 700 MHz NMR spectrometer (located at North Carolina State University, Raleigh, NC, USA) using a 5 mm cryogenically cooled ATMA inverse probe and ambient temperature of 25 ℃. A 1D NOESY presaturation pulse sequence (noesypr1d, [recycle delay (RD)-90°-t1-90°-tm-90°-acquire free induction decay (FID) was used for data acquisition. For each sample 16 transients were collected into 65k data points using a spectral width of 12.02 ppm, 2 s relaxation delay, 100 ms mixing time, and an acquisition time of 3.89 s per FID. The water resonance was suppressed using resonance irradiation during the relaxation delay and mixing time. NMR spectra were processed using TopSpin 3.2 software (Bruker-Biospin, Germany). Spectra were zero filled, and Fourier transformed after exponential multiplication with line broadening factor of 0.5. Phase and baseline of the spectra were manually corrected for each spectrum. Spectra were referenced internally to the DSS-d6 signal. The quality of each NMR spectrum was assessed for the level of noise and alignment of identified markers. Spectra were assessed for missing data and underwent quality checks. NMR bins (0.7-9.50 ppm) were created excluding water and urea (4.25- 6.5 ppm) using intelligent bucket integration of 0.04 ppm bucket width with 50% looseness using ACD NMR Processor (ACD Labs Inc, Toronto, Canada). Integrals of each of the bins were normalized to total integral of each of the spectrum.

Analysis:

Analysis ID:	AN000651
Analysis Type:	NMR
Num Factors:	3

NMR:

NMR ID:	NM000073
Analysis ID:	AN000651
Instrument Name:	Bruker Avance III
Instrument Type:	FT-NMR
NMR Experiment Type:	1D 1H
Spectrometer Frequency:	700 MHz