Summary of Study ST002402

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 PR001334. The data can be accessed directly via it's Project DOI: 10.21228/M88T45 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 IDST002402
Study TitleFour-dimensional trapped ion mobility spectrometry lipidomics for high throughput clinical profiling of human blood samples
Study TypeClinical Lipidomics
Study SummaryImplementation of operational workflows using untargeted high-resolution ion mobility mass spectrometry in clinical lipidomics require reproducible, high-throughput lipid extraction, high-quality lipid annotation, absolute quantification, and cross-validation. We present a high-throughput 4D-PASEF MS platform suitable for clinical plasma lipidomic profiling encompassing automated extraction, accurate lipid annotation, and reproducible quantification. Newly generated 4D-PASEF lipid descriptors (m/z, RT, CCS, MS2) of 200 lipid standards and of 493 lipid signals curated from reference plasma, along with qualification of reproducible features in replicate lipid extracts and dilution analyses enabled highly confident annotation, reaching 100% confidence, of 370 lipids from NIST SRM 1950 plasma and 364 lipids from NIST SRM 1951 serum. 359 plasma lipids were reproducibly quantified using absolute quantification, cross-validated by inter-instrument studies, and supported by inter-laboratory data. The high-throughput 4D-PASEF lipidomics platform was demonstrated by reproducible identification of intra-individual multidien lipidome phenotype in plasma, serum, blood, venous, and finger-prick dried blood spots.
Institute
University Medical Center of Mainz
Last NameBindila
First NameLaura
AddressDuesbergweg 6, 55128 Mainz, Germany
Emailbindila@uni-mainz.de
Phone+49 6131 39 25794
Submit Date2022-12-07
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2023-01-04
Release Version1
Laura Bindila Laura Bindila
https://dx.doi.org/10.21228/M88T45
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001334
Project DOI:doi: 10.21228/M88T45
Project Title:Clinical Lipidomic Profiling
Project Type:Clinical Lipidomics
Project Summary:Four-dimensional trapped ion mobility spectrometry lipidomics for high throughput clinical profiling of human blood samples
Institute:University Medical Center of Mainz
Department:Institute of Physiological Chemistry
Laboratory:Clinical Lipidomics Unit
Last Name:Bindila
First Name:Laura
Address:Duesbergweg 6, 55128 Mainz, Germany
Email:bindila@uni-mainz.de
Phone:49 6131 39 25794
Funding Source:BMBF-funded DIASyM project

Subject:

Subject ID:SU002491
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:26-60
Gender:Male and female
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Factor
SA239144220826_neg repetiton3_R9Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239145220826_neg repetiton3_R8Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239146220826_neg repetiton3_R10Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239147220826_neg repetiton3_R12Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239148220826_neg repetiton3_R13Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239149220826_neg repetiton3_R7Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239150220826_neg repetiton3_R11Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239151220826_neg repetiton3_R6Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239152220826_neg repetiton3_R2Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239153220826_neg repetiton3_R31Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239154220826_neg repetiton3_R1Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239155220826_neg repetiton3_R3Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239156220826_neg repetiton3_R5Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239157220826_neg repetiton3_R4Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239158220826_neg repetiton3_R14Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239159220826_neg repetiton3_R15Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239160220826_neg repetiton3_R24Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239161220826_neg repetiton3_R25Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239162220826_neg repetiton3_R23Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239163220826_neg repetiton3_R22Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239164220826_neg repetiton3_R20Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239165220826_neg repetiton3_R21Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239166220826_neg repetiton3_R26Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239167220826_neg repetiton3_R27Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239168220826_neg repetiton3_R17Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239169220826_neg repetiton3_R16Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239170220826_neg repetiton3_R18Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239171220826_neg repetiton3_R30Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239172220826_neg repetiton3_R28Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239173220826_neg repetiton3_R29Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239174220826_neg repetiton3_R19Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239175220826_neg repetiton3_R32Biological matrix - NIST Human Plasma Interday extraction plate 2_neg
SA239176220826_pos repetiton3_R14Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239177220826_pos repetiton3_R13Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239178220826_pos repetiton3_R12Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239179220826_pos repetiton3_R15Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239180220826_pos repetiton3_R16Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239181220826_pos repetiton3_R19Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239182220826_pos repetiton3_R18Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239183220826_pos repetiton3_R17Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239184220826_pos repetiton3_R11Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239185220826_pos repetiton3_R10Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239186220826_pos repetiton3_R6Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239187220826_pos repetiton3_R7Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239188220826_pos repetiton3_R8Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239189220826_pos repetiton3_R5Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239190220826_pos repetiton3_R4Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239191220826_pos repetiton3_R1Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239192220826_pos repetiton3_R2Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239193220826_pos repetiton3_R3Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239194220826_pos repetiton3_R20Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239195220826_pos repetiton3_R21Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239196220826_pos repetiton3_R29Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239197220826_pos repetiton3_R28Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239198220826_pos repetiton3_R9Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239199220826_pos repetiton3_R31Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239200220826_pos repetiton3_R32Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239201220826_pos repetiton3_R27Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239202220826_pos repetiton3_R30Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239203220826_pos repetiton3_R26Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239204220826_pos repetiton3_R22Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239205220826_pos repetiton3_R23Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239206220826_pos repetiton3_R24Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239207220826_pos repetiton3_R25Biological matrix - NIST Human Plasma Interday extraction plate 2_pos
SA239208220826_neg repetiton3_R46Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239209220826_neg repetiton3_R45Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239210220826_neg repetiton3_R47Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239211220826_neg repetiton3_R49Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239212220826_neg repetiton3_R42Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239213220826_neg repetiton3_R43Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239214220826_neg repetiton3_R48Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239215220826_neg repetiton3_R44Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239216220826_neg repetiton3_R54Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239217220826_neg repetiton3_R53Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239218220826_neg repetiton3_R55Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239219220826_neg repetiton3_R57Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239220220826_neg repetiton3_R58Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239221220826_neg repetiton3_R52Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239222220826_neg repetiton3_R51Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239223220826_neg repetiton3_R40Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239224220826_neg repetiton3_R41Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239225220826_neg repetiton3_R33Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239226220826_neg repetiton3_R39Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239227220826_neg repetiton3_R50Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239228220826_neg repetiton3_R59Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239229220826_neg repetiton3_R56Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239230220826_neg repetiton3_R36Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239231220826_neg repetiton3_R64Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239232220826_neg repetiton3_R38Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239233220826_neg repetiton3_R60Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239234220826_neg repetiton3_R35Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239235220826_neg repetiton3_R63Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239236220826_neg repetiton3_R61Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239237220826_neg repetiton3_R34Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239238220826_neg repetiton3_R62Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239239220826_neg repetiton3_R37Biological matrix - NIST Human Plasma Interday extraction plate 3_neg
SA239240220826_pos repetiton3_R36Biological matrix - NIST Human Plasma Interday extraction plate 3_pos
SA239241220826_pos repetiton3_R37Biological matrix - NIST Human Plasma Interday extraction plate 3_pos
SA239242220826_pos repetiton3_R34Biological matrix - NIST Human Plasma Interday extraction plate 3_pos
SA239243220826_pos repetiton3_R35Biological matrix - NIST Human Plasma Interday extraction plate 3_pos
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Collection:

Collection ID:CO002484
Collection Summary:1) NIST Human Plasma 1950 Standard Reference Material were purchased commercially 2) The different biological matrices selected for this purpose were plasma, serum, blood, Dried Blood Spot (DBS) from the vein, and DBS from the fingertip blood. For this, two blood samples, one in 9mL EDTA and the other in 7.5mL serum monovette, were collected from four volunteers of our laboratory and the authors of this study. For the plasma and serum analysis, the serum monovette was centrifuged at 4°C, 2000 g for 10 min directly after the blood was collected. The resulting upper plasma/serum phase pooled and transferred to 5mL brown Eppendorf tubes. From this pooled volume, three 20μL aliquots were collected into three 1.5 mL brown Eppendorf tubes (to avoid light-induced chemical changes). The tubes were then stored at -80°C until the extraction. For the whole blood analysis, before the centrifugation process, 20μL of blood from the EDTA tube was collected into 3 brown Eppendorf tubes each and placed on ice until the extraction (which was performed on the same day). For the DBS venous, 20μL of blood from the EDTA tube was spotted in the center of each three spots of a DBS card (GE Healthcare Bio-sciences, USA). A similar procedure was followed for the DBS finger except that the blood used for the spot was from the fingertip. For both the DBSs, the spots dried for 3-4 hours at room temperature until the spots have a homogeneous brown color and then stored at -20°C until the further procedure.
Collection Protocol Filename:LBlood_Sample_collection_Protocol.docx
Sample Type:Blood (whole)

Treatment:

Treatment ID:TR002503
Treatment Summary:Sample collection was performed from healthy individuals without any prior or ongoing treatment during the collection.

Sample Preparation:

Sampleprep ID:SP002497
Sampleprep Summary:In order to optimize the extraction efficiency of lipids, a liquid-liquid extraction (LLE) method based on MTBE/methanol (10:3; v/v) was adapted to high-throughput extraction, using the epMotion® 5070 liquid handling workstation. NIST SRM plasma were used for the optimization of lipid extraction and for the generation of replicate lipid extracts for 4D-PASEF method development. Therefore, 20 µl aliquots of each (plasma and serum) were pipetted into a 2ml deepwell plate (Eppendorf, Germany) and the plate was placed into the epMotion plate holder where all further extractions steps were carried out by the epMotion workstation. 615 µL cold MTBE, 185 µl cold MeOH, containing the spiking solution, as well as 250 µL cold FA (0.1%) was added to the samples. After 10 min vortexing of the samples in the workstation (8°C and 1050 rpm), the 2ml deepwell plate was centrifuged for a further 10 min (5000g swing out / 4°C). After placing the 2 ml deepwell plate back in the epMotion, the upper organic phase was transferred to a fresh 1 ml deepwell plate (Eppendorf, Germany) and subsequently evaporated under a gentle stream of nitrogen at 37°C in the Vapotherm (Barkey, Germany). Lipid extracts were reconstituted in 360 μL methanol/water (9:1; v/v) and transferred to a twinTec PCR injectplate (Eppendorf, Germany) for further LC/MS analysis. The remaining lipid extracts were evaporated to dryness and stored at -20 °C till further analysis. To minimize ex-vivo alterations of the endogenous lipid levels all extraction procedure steps, where implementable, were carried out at 4°C.
Sampleprep Protocol Filename:Sample_Preparation_Protocol.docx

Combined analysis:

Analysis ID AN003914 AN003915 AN003916
Analysis type MS MS MS
Chromatography type Reversed phase Reversed phase Reversed phase
Chromatography system Bruker UHPLC Bruker Elute UHPLC Agilent 1200
Column Phenomenex Luna Omega C18 (100 x 2.1mm,1.6um) Phenomenex Luna Omega C18 (100 x 2.1mm,1.6um) Ascentis Express C18 (100 x 2.1mm,2.7um)
MS Type ESI ESI ESI
MS instrument type timsTOF timsTOF Triple quadrupole
MS instrument name Bruker timsTOF Bruker timsTOF ABI Sciex 5500 QTrap
Ion Mode NEGATIVE POSITIVE UNSPECIFIED
Units Peak area Peak area Peak area

Chromatography:

Chromatography ID:CH002896
Chromatography Summary:negative ion mode
Methods Filename:Liquid_chromatography.docx
Instrument Name:Bruker UHPLC
Column Name:Phenomenex Luna Omega C18 (100 x 2.1mm,1.6um)
Column Temperature:45
Flow Gradient:The LC method consisted of a 20 min runtime with the following gradient: T0 to T1 – mobile phase A at 60% and mobile phase B at 40% which was then elevated to 90% mobile phase B and 10% mobile phase by T16 and up to 99% mobile phase B by T16.5 and then escalated back to 40% mobile phase B by T20
Flow Rate:200 µl/min
Solvent A:50% methanol/50% water; 0.1% formic acid; 7.5 mM ammonium formate, 0.1% triethylamine
Solvent B:20% methanol/80% isopropanol; 0.1% formic acid; 7.5 mM ammonium formate; 0.1% triethylamine
Chromatography Type:Reversed phase
  
Chromatography ID:CH002897
Chromatography Summary:positive ion mode
Methods Filename:Liquid_chromatography.docx
Instrument Name:Bruker Elute UHPLC
Column Name:Phenomenex Luna Omega C18 (100 x 2.1mm,1.6um)
Column Temperature:45
Flow Gradient:The LC method consisted of a 20 min runtime with the following gradient: T0 to T1 – mobile phase A at 60% and mobile phase B at 40% which was then elevated to 90% mobile phase B and 10% mobile phase by T16 and up to 99% mobile phase B by T16.5 and then escalated back to 40% mobile phase B by T20
Flow Rate:200 µl/min
Solvent A:50% methanol/50% water; 0.1% formic acid; 7.5 mM ammonium formate
Solvent B:20% methanol/80% isopropanol; 0.1% formic acid; 7.5 mM ammonium formate
Chromatography Type:Reversed phase
  
Chromatography ID:CH002898
Chromatography Summary:positive/negative ion modes
Methods Filename:Liquid_chromatography.docx
Instrument Name:Agilent 1200
Column Name:Ascentis Express C18 (100 x 2.1mm,2.7um)
Column Temperature:45
Flow Gradient:Gradient elution began at 40% B, held for 3 min and was then linearly increased over 42 min to 90% B, then linearly increased to 99% B in 1 min, held there for 7 min and decreased over 2 min to 40% B.
Flow Rate:200 µl/min
Solvent A:50% methanol/50% water; 0.1% formic acid; 7.5 mM ammonium formate, 0.1% triethylamine
Solvent B:20% methanol/80% isopropanol; 0.1% formic acid; 7.5 mM ammonium formate; 0.1% triethylamine
Chromatography Type:Reversed phase

MS:

MS ID:MS003653
Analysis ID:AN003914
Instrument Name:Bruker timsTOF
Instrument Type:timsTOF
MS Type:ESI
MS Comments:The instrumental calibrations and the data acquisition were controlled by timsControl 2. The identification of the lipid molecules using the filters mentioned above was performed on Metaboscape 2021a. After the identification via the ClinLip Analyte list, the annotated bucket table was exported to the MS excel 2019 and all the quantifications were performed there-in.
Ion Mode:NEGATIVE
Analysis Protocol File:MS_Conditions.docx
  
MS ID:MS003654
Analysis ID:AN003915
Instrument Name:Bruker timsTOF
Instrument Type:timsTOF
MS Type:ESI
MS Comments:The instrumental calibrations and the data acquisition were controlled by timsControl 2. The identification of the lipid molecules using the filters mentioned above was performed on Metaboscape 2021a. After the identification via the ClinLip Analyte list, the annotated bucket table was exported to the MS excel 2019 and all the quantifications were performed there-in.
Ion Mode:POSITIVE
Analysis Protocol File:MS_Conditions.docx
  
MS ID:MS003655
Analysis ID:AN003916
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Targeted MRM transitions were acquired in positive and negative ion mode using polarity switching via Analyst 1.6.2 software. Quantification was performed via MultiQuant 3.0 quantitation package.
Ion Mode:UNSPECIFIED
Analysis Protocol File:MS_Conditions.docx
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