Summary of Study ST000545

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 PR000399. The data can be accessed directly via it's Project DOI: 10.21228/M8GG6B This work is supported by NIH grant, U2C- DK119886.

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

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST000545
Study TitleCHEAR Plasma Reference Material Proficiency Test Biocrates
Study TypeMetabolomics
Study SummaryCHEAR Reference Material Plasma was provided by Emory University. The material was prepared and analyzed by way of LC-MS and Biocrates workflow employed by the Eastern Regional Metabolomics Resource Core (protocols available in metabolomics workbench). Six samples were injected of the sample reference material prepared in replicate.
Institute
RTI International
DepartmentDiscovery-Sciences-Technology (DST)
LaboratoryRTI CHEAR Analytical Hub - Untargeted Analysis Resource Core
Last NameFennell
First NameTimothy
Address3040 E Cornwallis Road, Research Triangle Park, NC 27709
Emailfennell@rti.org
Phone919-485-2781
Submit Date2016-12-29
Raw Data AvailableYes
Raw Data File Type(s)wiff
Chear StudyYes
Analysis Type DetailLC-MS
Release Date2024-12-31
Release Version1
Timothy Fennell Timothy Fennell
https://dx.doi.org/10.21228/M8GG6B
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000399
Project DOI:doi: 10.21228/M8GG6B
Project Title:CHEAR Plasma Reference Material Proficiency Test Biocrates
Project Type:CHEAR-UT-1
Project Summary:CHEAR Reference Material Plasma was provided by Emory University. The material was prepared and analyzed by way of LC-MS and Biocrates workflow employed by the Eastern Regional Metabolomics Resource Core (protocols available in metabolomics workbench). Six samples were injected of the sample reference material prepared in replicate.
Institute:RTI International
Department:Discovery-Science-Technology
Laboratory:RTI CHEAR Analytical Hub - Untargeted Analysis Resource Core (UARC)
Last Name:Fennell
First Name:Timothy
Address:3040 E Cornwallis Road, Research Triangle Park, NC 27709
Email:fennell@rti.org
Phone:919-485-2781

Subject:

Subject ID:SU000567
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 Sample Type
SA028126p180 Cal5Control
SA028127p180 Cal4Control
SA028128p180 Cal3Control
SA028129p180 Cal6Control
SA028130p180 QC1Control
SA028131p180 QC3Control
SA028132p180 QC2Control
SA028133p180 Cal2Control
SA028134p180 Cal7Control
SA028135p180 Cal1Control
SA028136PBS_01Control
SA028137PBS_02Control
SA028138PBS_03Control
SA028139PP_A_09_3Replicate
SA028140PP_A_09_2Replicate
SA028141PP_A_09_4Replicate
SA028142PP_A_09_6Replicate
SA028143PP_A_09_1Replicate
SA028144PP_A_09_5Replicate
Showing results 1 to 19 of 19

Collection:

Collection ID:CO000561
Collection Summary:CHEAR Reference Material Plasma was provided by Emory University.
Sample Type:Blood

Treatment:

Treatment ID:TR000581
Treatment Summary:No treatment

Sample Preparation:

Sampleprep ID:SP000574
Sampleprep Summary:Parent Aliquots were quickly prepared in the 4°C room using the Drummond pipet aid and serological pipet. 40 mL plasma were transferred to 50 mL tubes in 4°C room and capped immediately and placed on ice. If needed, the bulk plasma was mixed in between aliquots. The parent aliquots were labeled appropriately. Sub-Aliquots were prepared on ice at the bench. The parent aliquots were mixed by inverting the tube thoroughly before and in between aliquots as needed. 1 mL plasma was transferred to cryovials and capped immediately and stored on ice until sample splitting was competed. The sub aliquots were labeled appropriately. Sub-aliquots were stored at -80°C. Plasma Aliquots for LCMS platforms: Used sub-aliquot “PP_A_09” to prepare aliquots for various LCMS platforms. Allowed sub-aliquot to thaw on ice for 30 – 60 min. Vortexed aliquot briefly on vortexer, centrifuged at 4 °C for 2 minutes at 16,000 rcf. Aliquoted out 6 tubes for Biocrates from “PP_A_09”. Aliquots were stored at -80 °C until analysis. Sample preparation for Biocrates Plate: CHEAR plasma samples were thawed on ice for 30–60 min. All samples were vortexed on a multi-tube vortexer for 4 mins at 5,000 rpm and centrifuged at 4 °C for 5 minutes at 16,000 rcf before loading on the p180 plate. The samples were then placed on ice in the analysis order for sample loading on the p180 Biocrates plate.   Biocrates Plate Preparation: A Biocrates p180 kit was prepared following the AbsoluteIDQ™ p180 Kit metabolomics procedure. Briefly, an internal standard mix was added to 95 of the 96 wells. Next, zero samples, QC standards and calibration standards were added to their corresponding wells. The samples (20 µL) were then added to the appropriate wells and dried for 30 minutes under nitrogen flow. The plate was derivatized using a 5% phenylisothiocyanate (PITC) solution in (1:1:1) ethanol:pyridine:water and, then, incubated for 20 minutes followed by a drying step under nitrogen flow. An extraction solvent (5 mM ammonium acetate in methanol) was added to all wells. The plate was then shaken and centrifuged. After centrifugation, 150 µL was removed and transferred to a second 96-well plate (LCMS plate). This second plate was diluted with 150 µL of HPLC grade water for a subsequent LCMS (MRM analysis) for measuring amino acids and biogenic amines. All wells in the original plate were diluted with 400 µL of flow injection analysis (FIA) Running Solvent for a FIA-MS (MRM analysis) for measuring lipids, acylcarnitines, and hexose.

Combined analysis:

Analysis ID AN000829 AN000830 AN000831
Analysis type MS MS MS
Chromatography type Reversed phase Flow induction analysis Flow induction analysis
Chromatography system Agilent 1100 Agilent 1100 Agilent 1100
Column Agilent Eclipse XDB-C18 (100 x 3.0mm,3.5um) No column No column
MS Type ESI ESI ESI
MS instrument type Triple quadrupole Triple quadrupole Triple quadrupole
MS instrument name ABI Sciex 4000 QTrap ABI Sciex 4000 QTrap ABI Sciex 4000 QTrap
Ion Mode POSITIVE POSITIVE NEGATIVE
Units um um um

Chromatography:

Chromatography ID:CH000593
Instrument Name:Agilent 1100
Column Name:Agilent Eclipse XDB-C18 (100 x 3.0mm,3.5um)
Column Pressure:30-120 bar
Column Temperature:50 degrees C
Flow Rate:0.5mL/min
Sample Injection:10uL
Solvent A:100% water; 0.2% formic acid
Solvent B:100% acetonitrile; 0.2% formic acid
Analytical Time:9.5 minutes
Target Sample Temperature:10 degrees C
Sample Loop Size:100uL
Chromatography Type:Reversed phase
  
Chromatography ID:CH000594
Instrument Name:Agilent 1100
Column Name:No column
Column Pressure:4-50 bar
Sample Injection:20uL
Solvent B:100% methanol
Analytical Time:3.0 minutes
Target Sample Temperature:10 degrees C
Sample Loop Size:100uL
Chromatography Type:Flow induction analysis

MS:

MS ID:MS000730
Analysis ID:AN000829
Instrument Name:ABI Sciex 4000 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:POSITIVE
Collision Gas:Medium
Ion Spray Voltage:5500
  
MS ID:MS000731
Analysis ID:AN000830
Instrument Name:ABI Sciex 4000 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:POSITIVE
Collision Gas:Medium
Ion Spray Voltage:5500
  
MS ID:MS000732
Analysis ID:AN000831
Instrument Name:ABI Sciex 4000 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:NEGATIVE
Collision Gas:Medium
Ion Spray Voltage:-4500
  logo