Summary of study ST000825

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 PR000587. The data can be accessed directly via it's Project DOI: 10.21228/M8SQ3D This work is supported by NIH grant, U2C- DK119886.

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Study IDST000825
Study TitleCHEAR Christiani Biocrates
Study SummaryHuman cord blood serum samples (200) were provided by David Christiani. The 200 study samples, total pool samples, and external CHEAR Plasma Reference Material samples were prepared and analyzed using the Biocrates AbsoluteIDQ p180 Kit.
Institute
RTI International
DepartmentACP
LaboratoryRTI CHEAR Analytical Hub - Untargeted Analysis Resource Core (UARC)
Last NameFennell
First NameTimothy
Address3040 E Cornwallis Rd, Durham, North Carolina, 27709, USA
Emailfennell@rti.org
Phone919-485-2781
Submit Date2017-07-18
Total Subjects200
Study CommentsCHEAR Plasma Reference Material samples were aliquots of sub-aliquots that came from parent aliquots that were made from original stock.
Raw Data AvailableYes
Raw Data File Type(s).wiff
Chear StudyYes
Analysis Type DetailLC-MS
Release Date2019-09-23
Release Version1
Timothy Fennell Timothy Fennell
https://dx.doi.org/10.21228/M8SQ3D
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000587
Project DOI:doi: 10.21228/M8SQ3D
Project Title:CHEAR Christiani Biocrates
Project Summary:Human cord blood serum samples (200) were provided by David Christiani. The 200 study samples, total pool samples, and external CHEAR Plasma Reference Material samples were prepared and analyzed using the Biocrates AbsoluteIDQ p180 Kit.
Institute:RTI International
Department:ACP
Laboratory:RTI CHEAR Analytical Hub - Untargeted Analysis Resource Core (UARC)
Last Name:Fennell
First Name:Timothy
Address:3040 E Cornwallis Rd, Durham, North Carolina, 27709, USA
Email:fennell@rti.org
Phone:919-485-2781

Subject:

Subject ID:SU000851
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Human

Factors:

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

mb_sample_id local_sample_id sample data
SA045879C-S58F8-S-02data
SA045880p180 QC2_03_plate1702data
SA045881p180 QC2_02_plate1702data
SA045882Biocrates Total Pool 15data
SA045883C-SB7K0-S-02data
SA045884C-N8KQ4-S-02data
SA045885C-NL6M0-S-02data
SA045886p180 QC2_01_plate1702data
SA045887p180 Cal6_plate1702data
SA045888p180 Cal2_plate1702data
SA045889p180 Cal1_plate1702data
SA045890PBS_03_plate1702data
SA045891p180 Cal3_plate1702data
SA045892p180 Cal4_plate1702data
SA045893C-U9LA9-S-02data
SA045894p180 Cal5_plate1702data
SA045895p180 Cal7_plate1702data
SA045896CHEAR Reference Plasma 15data
SA045897C-QCPY4-S-02data
SA045898C-J2DF2-S-02data
SA045899C-MFXB4-S-02data
SA045900CHEAR Reference Plasma 16data
SA045901C-XUPK8-S-02data
SA045902C-S6ZN4-S-02data
SA045903C-KNVW4-S-02data
SA045904C-NXNQ0-S-02data
SA045905C-GXF72-S-02data
SA045906C-Y5941-S-02data
SA045907C-W9RY8-S-02data
SA045908PBS_02_plate1702data
SA045909C-XDYH3-S-02data
SA045910C-XJJ07-S-02data
SA045911Biocrates Total Pool 16data
SA045912C-KBHQ8-S-02data
SA045913C-NTCH0-S-02data
SA045914PBS_01_plate1702data
SA045915C-SNM00-S-02data
SA045916C-M4GD6-S-02data
SA045917C-SD2X1-S-02data
SA045918C-QP2F7-S-02data
SA045919C-JPU80-S-02data
SA045920C-QS0G0-S-02data
SA045921Biocrates Total Pool 13data
SA045922CHEAR Reference Plasma 12data
SA045923C-HKPH3-S-02data
SA045924Biocrates Total Pool 12data
SA045925C-X1ZY6-S-02data
SA045926C-KCXU1-S-02data
SA045927C-KYRT0-S-02data
SA045928C-H78F5-S-02data
SA045929C-WH892-S-02data
SA045930C-URD82-S-02data
SA045931C-PURL2-S-02data
SA045932C-UY789-S-02data
SA045933C-PU1K7-S-02data
SA045934C-N3BN0-S-02data
SA045935Biocrates Total Pool 14data
SA045936C-Z9M00-S-02data
SA045937C-H4KC0-S-02data
SA045938CHEAR Reference Plasma 14data
SA045939C-QJ3B8-S-02data
SA045940C-KHU38-S-02data
SA045941C-YF3W3-S-02data
SA045942C-XC0R5-S-02data
SA045943C-W74S5-S-02data
SA045944CHEAR Reference Plasma 13data
SA045945C-LSVC6-S-02data
SA045946C-L09R9-S-02data
SA045947C-UK244-S-02data
SA045948C-GY7T1-S-02data
SA045949C-YT9Y1-S-02data
SA045950C-JG1G3-S-02data
SA045951C-K2CP0-S-02data
SA045952C-VBBW0-S-02data
SA045953C-HHLS9-S-02data
SA045954Biocrates Total Pool 21data
SA045955C-HZ9K6-S-02data
SA045956C-JY095-S-02data
SA045957C-TKCG6-S-02data
SA045958CHEAR Reference Plasma 20data
SA045959C-KDJS6-S-02data
SA045960Biocrates Total Pool 20data
SA045961C-K39B9-S-02data
SA045962C-HHEB4-S-02data
SA045963C-VVU44-S-02data
SA045964C-YF9D8-S-02data
SA045965C-HH3D7-S-02data
SA045966C-Y7GG1-S-02data
SA045967C-QAQF9-S-02data
SA045968p180 Cal6_plate1703data
SA045969p180 Cal5_plate1703data
SA045970p180 Cal4_plate1703data
SA045971p180 Cal7_plate1703data
SA045972p180 QC2_01_plate1703data
SA045973p180 QC2_03_plate1703data
SA045974p180 QC2_02_plate1703data
SA045975p180 Cal3_plate1703data
SA045976p180 Cal2_plate1703data
SA045977CHEAR Reference Plasma 21data
SA045978C-Z9QK7-S-02data
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Collection:

Collection ID:CO000845
Collection Summary:All samples stored at -80°C.
Sample Type:Serum (human), Plasma (human)
Storage Conditions:-80°C

Treatment:

Treatment ID:TR000865
Treatment Summary:N/A

Sample Preparation:

Sampleprep ID:SP000858
Sampleprep Summary:Sample Preparation Prior to Biocrates p180 Kit Plate Analysis: External CHEAR Reference Material- Plasma: Parent and Sub-Aliquots: The CHEAR PlasmaRef_20160726 (500 mL) was removed from -80°C storage and thawed by storing it at 4°C overnight. The following day, the thawed plasma was inspected to ensure there was no ice remaining and the bulk plasma was then mixed in the 4°C room by repeatedly inverting the container. Parent Aliquots were quickly prepared in the 4°C room using the Drummond pipet aid and serological pipet. 40 mL plasma aliquots 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 aliquots were 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 Biocrates platform: The sub-aliquot of CHEAR PlasmaRef_20160726 PP_A_08 was used to prepare aliquots for the Biocrates platform. PP_A_08 was thawed on ice for 30 – 60 min and vortexed briefly on a vortexer, followed by centrifugation at 4°C for 2 minutes at 16,000 rcf. A total of 21 aliquots of 22 µL volumes were prepared as external pool samples for the Biocrates analysis from PP_A_08. These external pool samples were named CHEAR Reference Plasma 1 through 21. Aliquots were stored at -80°C until analysis. CHEAR Christiani Human Cord Blood Serum Samples: Each received sample was transferred from its straw to a new, pre-labeled Lo-bind tube. A volume of 5 µL was transferred from each sample to a new, pre-labeled 7-mL tube to create the total pool sample. The total pool underwent vortex mixing before creating 21 aliquots of 22 µL volumes that were to be used as total pool samples. These total pool samples were named Biocrates Total Pool 1 through 21. Aliquots were stored at -80°C until analysis. Sample preparation for Biocrates Plate: CHEAR Christiani samples, CHEAR Plasma Reference Material external pool samples and Christiani total pool samples were thawed on ice for 30–60 min and placed on ice in the analysis order for sample loading on the p180 Biocrates plate. Biocrates Plate Preparation: A total of three Biocrates plates (1701, 1702, and 1703) were used to accommodate all samples and were prepared following the procedure of AbsoluteIDQ™ p180 Kit. For each plate, the isotope labeled internal standard mix was added to 95 of the 96 wells. The zero sample, QC standards and calibration standards were added to their corresponding wells. A volume of 20 µL of each sample was then added to the appropriate well and dried for 30 minutes under nitrogen flow. All samples were derivatized by adding a 5% solution of phenylisothiocyanate (PITC) in ethanol/pyridine/water (1:1:1, v/v/v) through incubation for 20 min at room temperature and then drying under nitrogen flow. An extraction solvent (5 mM ammonium acetate in methanol) was added to all the wells. After shaking and centrifugation through a filter membrane on this plate, 150 µL solution was transferred to a new, 96-well plate and diluted with 150 µL of HPLC grade water for LC-MS analysis to measure amino acids and biogenic amines. The remaining solution in the original plate was diluted with 400 µL of flow injection analysis (FIA) running solvent for FIA-MS analysis to measure lipids, acylcarnitines, and hexose. The Multiple Reaction Monitoring (MRM) mode was used for both LC-MS and FIA-MS analyses.

Combined analysis:

Analysis ID AN001311 AN001312 AN001313
Analysis type MS MS MS
Chromatography type Reversed phase Isocratic Isocratic
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:CH000918
Chromatography Summary:Reverse Phase Gradient separation
Instrument Name:Agilent 1100
Column Name:Agilent Eclipse XDB-C18 (100 x 3.0mm,3.5um)
Column Pressure:30-120 bar
Column Temperature:50°C
Flow Rate:0.5 mL/min
Sample Injection:10 µL
Target Sample Temperature:10 °C
Sample Loop Size:100 µL
Randomization Order:Yes
Chromatography Type:Reversed phase
  
Chromatography ID:CH000919
Chromatography Summary:FIA analysis
Instrument Name:Agilent 1100
Column Name:no column
Sample Injection:20 µL
Target Sample Temperature:10 °C
Sample Loop Size:100 µL
Randomization Order:Yes
Chromatography Type:Isocratic

MS:

MS ID:MS001204
Analysis ID:AN001311
Instrument Name:ABI Sciex 4000 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:POSITIVE
Collision Gas:Medium
Ion Source Temperature:500°C
Ion Spray Voltage:5500
  
MS ID:MS001205
Analysis ID:AN001312
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:MS001206
Analysis ID:AN001313
Instrument Name:ABI Sciex 4000 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:NEGATIVE
Collision Gas:Medium
Ion Spray Voltage:-4500
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