Summary of Study ST000605

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 PR000442. The data can be accessed directly via it's Project DOI: 10.21228/M8XC7Q This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST000605
Study TitleWhole blood reveals more metabolic detail of the human metabolome than serum as measured by 1H-NMR spectroscopy: Implications for sepsis metabolomics
Study TypeSingle timepoint; healthy controls
Study SummaryHealthy volunteers
Institute
University of Michigan
DepartmentClinical Pharmacy
LaboratoryThe NMR Metabolomics Laboratory (Stringer)
Last NameStringer
First NameKathleen
AddressUniversity of Michigan, 2900 Huron Parkway, Ann Arbor, MI 48105
EmailNMRmetabolomics@umich.edu
PhoneNA
Submit Date2016-12-08
Total Subjects19 whole blood; 20 serum
Raw Data AvailableYes
Raw Data File Type(s)fid
Analysis Type DetailNMR
Release Date2017-01-06
Release Version1
Kathleen Stringer Kathleen Stringer
https://dx.doi.org/10.21228/M8XC7Q
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000442
Project DOI:doi: 10.21228/M8XC7Q
Project Title:Whole blood and serum 1D-1H-NMR metabolomics
Project Type:Cross-center Quantitative NMR Urine Metabolomics Study
Project Summary:Serum is a common sample of convenience for metabolomics studies. Its processing time can be lengthy and may result in the loss of metabolites including those of red blood cells (RBC). Unlike serum, whole blood (WB) can be quickly processed, minimizing the influence of hemolysis without excluding RBC metabolites. To determine differences between serum and WB metabolomes, both sample types, collected from healthy volunteers, were assayed by 1H-NMR spectroscopy. A total of 34 and 51 aqueous metabolites were quantified from serum and WB, respectively. Free hemoglobin (Hgb) levels in serum were measured and the correlation between Hgb and serum metabolites was determined. All metabolites detected in serum were detected at higher concentrations in WB with the exception of acetoacetate and propylene glycol. The 18 unique metabolites of WB included adenosine, AMP, ADP and ATP, which are associated with RBC metabolism. The use of serum results in the underrepresentation of a number of metabolic pathways including branched chain amino acid degradation and glycolysis and gluconeogenesis. The range of free Hgb in serum was 0.03-0.010 g/dL and 8 metabolites were associated (p < 0.05) with free Hgb. The range of free Hgb in serum samples from 18 sepsis patients was 0.02-0.46 g/dL. WB and serum have unique aqueous metabolite profiles but the use of serum may introduce potential pathway bias. Use of WB for metabolomics may be particularly important for studies in diseases like sepsis in which RBC metabolism is altered and mechanical and sepsis-induced hemolysis contributes to variance in the metabolome. This study has been published: Shock 2015;44:200-208.
Institute:University of Michigan;University of Mississippi
Department:Emergency Medicine
Laboratory:NMR Metabolomics Laboratory, University of Michigan
Last Name:Stringer
First Name:Kathleen
Address:College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, MI 48109
Email:NMRmetabolomics@umich.edu
Phone:NA
Funding Source:NIH (GM069438, GM113041); Upjohn Award, College of Pharmacy

Subject:

Subject ID:SU000628
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:Healthy - Mean (±SD): 54.9±8.2 years | Sepsis - Mean (+SD): 54.7±17.3 years
Weight Or Weight Range:Healthy - Mean (+SD): 74.4±1.71 kg; BMI < 30
Height Or Height Range:Healthy - Mean (±SD): 171.8±10.3cm
Gender:Healthy - males and females | Sepsis - males and females
Human Race:Healthy - Caucasian (C) and African American (AA) | Sepsis - Caucasian (C) and African American (AA)
Human Medications:Healthy - None
Human Prescription Otc:Healthy - None
Human Smoking Status:Healthy - Non smokers
Human Alcohol Drug Use:Healthy - None
Human Inclusion Criteria:Healthy - non-smoking, non-obese with no known medical conditions that require chronic drug therapy | Sepsis - admitted to emergency department or intensive care unit. Clinical indices for severe sepsis or septic shock were met: confirmed or suspected infection, two or more criteria of systemic inflammatory response criteria, and hypoperfusion evidenced by either a systolic blood pressure of <90mmHg after 20 min of fluid resuscitation or a blood lactate level of at least 36 mg/dL.
Species Group:Human

Factors:

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

mb_sample_id local_sample_id Sample Type Gender Race
SA033398CCMB13SSerum F AA
SA033399CCMB08SSerum F AA
SA033400CCMB09SSerum F C
SA033401CCMB11SSerum F C
SA033402CCMB10SSerum F C
SA033403CCMB07SSerum F C
SA033404CCMB16SSerum F C
SA033405CCMB02SSerum F C
SA033406CCMB20SSerum F C
SA033407CCMB06SSerum F C
SA033408CCMB18SSerum M C
SA033409CCMB01SSerum M C
SA033410CCMB19SSerum M C
SA033411CCMB17SSerum M C
SA033412CCMB03SSerum M C
SA033413CCMB15SSerum M C
SA033414CCMB05SSerum M C
SA033415CCMB04SSerum M C
SA033416CCMB12SSerum M C
SA033417CCMB14SSerum M C
SA033418CCMB08WBWhole Blood F AA
SA033419CCMB13WBWhole Blood F AA
SA033420CCMB09WBWhole Blood F C
SA033421CCMB11WBWhole Blood F C
SA033422CCMB10WBWhole Blood F C
SA033423CCMB20WBWhole Blood F C
SA033424CCMB16WBWhole Blood F C
SA033425CCMB07WBWhole Blood F C
SA033426CCMB02WBWhole Blood F C
SA033427CCMB06WBWhole Blood F C
SA033428CCMB17WBWhole Blood M C
SA033429CCMB19WBWhole Blood M C
SA033430CCMB18WBWhole Blood M C
SA033431CCMB01WBWhole Blood M C
SA033432CCMB04WBWhole Blood M C
SA033433CCMB03WBWhole Blood M C
SA033434CCMB05WBWhole Blood M C
SA033435CCMB12WBWhole Blood M C
SA033436CCMB14WBWhole Blood M C
SA033437CCMB15WBWhole Blood M C
Showing results 1 to 40 of 40

Collection:

Collection ID:CO000622
Collection Summary:Healthy - Direct venipuncture collection of WB and Serum from healthy controls | Sepsis - Indwelling arterial or venous catheter
Collection Protocol Comments:Healthy - Fasting (12h) blood samples (serum and whole blood) were collected between 8:30-9:30am by single direct venipuncture. | Sepsis - Serum generated via indwelling catheters as part of clinical trial (NCT 00372502)
Sample Type:Healthy - Blood: Whole Blood and Serum | Sepsis - Blood serum
Collection Method:Healthy - Direct venipuncture | Sepsis - indwelling catheters
Collection Location:Healthy - Michigan Clinical Research Unit | Sepsis - University of Mississippi
Collection Frequency:Healthy - 1 | Sepsis - 1
Collection Time:Healthy - Fasting, between 0830-0930 | Sepsis - N/A
Storage Conditions:Healthy - Serum: Initial RT then -80°C following processing (within 2h) Whole blood: Initial 0°C then -80°C following processing (within 10mins) | Sepsis - Initial RT then -80°C following processing (within 2h)
Storage Vials:Healthy - SST: Becton-Dickinson vacutainer Serum Separator tubes. WB: Becton-Dickinson vacutainer Sodium Heparin tubes | Sepsis - SST: Becton-Dickinson vacutainer Serum Separator tubes
Collection Tube Temp:Healthy - RT | Sepsis - RT
Additives:Healthy - Serum: none. Whole blood: Sodium Heparin | Sepsis - none
Blood Serum Or Plasma:Healthy - Whole blood and Serum | Sepsis - Serum

Treatment:

Treatment ID:TR000642
Treatment Summary:No treatment

Sample Preparation:

Sampleprep ID:SP000635
Sampleprep Summary:Methanol:cholorform extraction, filtration
Sampleprep Protocol Comments:Lipid fractions saved, stored at -20°C
Processing Method:Methanol:Chloroform Extraction, filtration
Processing Storage Conditions:0-4°C
Extraction Method:Methanol:chloroform extraction
Extract Enrichment:Ultra-filtration to remove residual protein
Extract Cleanup:N/A
Extract Storage:-80°C
Sample Resuspension:500 uL Deuterium Oxide (D2O)
Sample Spiking:DSS-IS2 (Chenomx, Inc)

Analysis:

Analysis ID:AN000926
Laboratory Name:University of Michigan Biochemical NMR Core Laboratory
Analysis Type:NMR
Acquisition Date:5/29/2013, 3/17/2014, 3/19/2014, 3/20/2014,7/29/2014, 8/28/2014
Acquisition Parameters File:metnoesy
Software Version:VNMRJ 3.2
Operator Name:Michael Finkel, Julie Trexel
Data Format:.fid
Num Factors:6
Num Metabolites:53
Units:uM

NMR:

NMR ID:NM000103
Analysis ID:AN000926
Instrument Name:Agilent 500/54 Premium Shielded VNMRS system
Instrument Type:FT-NMR
NMR Experiment Type:1D 1H
Standard Concentration:10% (~0.5mM)
Spectrometer Frequency:500 MHz
NMR Probe:ONE-Probe
NMR Solvent:D2O
NMR Tube Size:5mm
Shimming Method:Auto shim (gradient shimming), manual when necessary.
Pulse Sequence:1D-NOESY
Water Suppression:saturation at 80 Hz induced field strength
Pulse Width:5.5ms
Offset Frequency:around -178Hz
Chemical Shift Ref Cpd:DSS-d6 (whole blood), Formate (serum)
Temperature:25°C
Baseline Correction Method:manual
Chemical Shift Ref Std:DSS-d6 (whole blood), Formate (serum)
Binned Increment:N/A
Binned Data Protocol File:N
A
Binned Data Excluded Range:N/A
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