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.
Study ID | ST000605 |
Study Title | Whole blood reveals more metabolic detail of the human metabolome than serum as measured by 1H-NMR spectroscopy: Implications for sepsis metabolomics |
Study Type | Single timepoint; healthy controls |
Study Summary | Healthy volunteers |
Institute | University of Michigan |
Department | Clinical Pharmacy |
Laboratory | The NMR Metabolomics Laboratory (Stringer) |
Last Name | Stringer |
First Name | Kathleen |
Address | University of Michigan, 2900 Huron Parkway, Ann Arbor, MI 48105 |
NMRmetabolomics@umich.edu | |
Phone | NA |
Submit Date | 2016-12-08 |
Total Subjects | 19 whole blood; 20 serum |
Raw Data Available | Yes |
Raw Data File Type(s) | fid |
Analysis Type Detail | NMR |
Release Date | 2017-01-06 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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: | Mammals |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
mb_sample_id | local_sample_id | Sample Type | Gender | Race |
---|---|---|---|---|
SA033398 | CCMB13S | Serum | F | AA |
SA033399 | CCMB08S | Serum | F | AA |
SA033400 | CCMB09S | Serum | F | C |
SA033401 | CCMB11S | Serum | F | C |
SA033402 | CCMB10S | Serum | F | C |
SA033403 | CCMB07S | Serum | F | C |
SA033404 | CCMB16S | Serum | F | C |
SA033405 | CCMB02S | Serum | F | C |
SA033406 | CCMB20S | Serum | F | C |
SA033407 | CCMB06S | Serum | F | C |
SA033408 | CCMB18S | Serum | M | C |
SA033409 | CCMB01S | Serum | M | C |
SA033410 | CCMB19S | Serum | M | C |
SA033411 | CCMB17S | Serum | M | C |
SA033412 | CCMB03S | Serum | M | C |
SA033413 | CCMB15S | Serum | M | C |
SA033414 | CCMB05S | Serum | M | C |
SA033415 | CCMB04S | Serum | M | C |
SA033416 | CCMB12S | Serum | M | C |
SA033417 | CCMB14S | Serum | M | C |
SA033418 | CCMB08WB | Whole Blood | F | AA |
SA033419 | CCMB13WB | Whole Blood | F | AA |
SA033420 | CCMB09WB | Whole Blood | F | C |
SA033421 | CCMB11WB | Whole Blood | F | C |
SA033422 | CCMB10WB | Whole Blood | F | C |
SA033423 | CCMB20WB | Whole Blood | F | C |
SA033424 | CCMB16WB | Whole Blood | F | C |
SA033425 | CCMB07WB | Whole Blood | F | C |
SA033426 | CCMB02WB | Whole Blood | F | C |
SA033427 | CCMB06WB | Whole Blood | F | C |
SA033428 | CCMB17WB | Whole Blood | M | C |
SA033429 | CCMB19WB | Whole Blood | M | C |
SA033430 | CCMB18WB | Whole Blood | M | C |
SA033431 | CCMB01WB | Whole Blood | M | C |
SA033432 | CCMB04WB | Whole Blood | M | C |
SA033433 | CCMB03WB | Whole Blood | M | C |
SA033434 | CCMB05WB | Whole Blood | M | C |
SA033435 | CCMB12WB | Whole Blood | M | C |
SA033436 | CCMB14WB | Whole Blood | M | C |
SA033437 | CCMB15WB | Whole 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 |