Summary of Study ST003514

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 PR002159. The data can be accessed directly via it's Project DOI: 10.21228/M8JK0Q 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	ST003514
Study Title	Highly reliable LC-MS lipidomics database for efficient human plasma profiling based on NIST SRM 1950
Study Summary	Liquid chromatography coupled to high resolution mass spectrometry (LC-HRMS)-based methods have become the gold standard methodology for the comprehensive profiling of the human plasma lipidome. However, both the complexity of lipid chemistry and LC-HRMS-associated data pose challenges to the characterization of this biological matrix. In accordance with the current consensus of quality requirements for LC-HRMS lipidomics data, we aimed to characterize the NIST® Standard Reference Material for Human Plasma (SRM 1950) using an LC-ESI(+/–)-MS method compatible with high-throughput lipidome profiling. We generated a highly curated lipid database with increased coverage, quality, and consistency, including additional quality assurance procedures involving adduct formation, within-method m/z evaluation, retention behavior of species within lipid chain isomers, and expert-driven resolution of isomeric and isobaric interferences. As a proof-of-concept, we showed the utility of our in-house LC-MS lipidomic database –consisting of 592 lipid entries– for the fast, comprehensive, and reliable lipidomic profiling of the human plasma from healthy human volunteers. We are confident that the implementation of this robust resource and methodology will have a significant impact by reducing data redundancy and the current delays and bottlenecks in untargeted plasma lipidomic studies.
Institute	Universidad CEU San Pablo
Department	Chemistry and Biochemistry
Laboratory	CEMBIO
Last Name	Martínez
First Name	Sara
Address	Urbanización Montepríncipe, 28660, Boadilla del Monte, Madrid, Spain
Email	sara.martinezlopez@ceu.es
Phone	(+34)913724769
Submit Date	2024-07-01
Num Groups	1
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2024-10-11
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR002159
Project DOI:	doi: 10.21228/M8JK0Q
Project Title:	Highly reliable LC-MS lipidomics database for efficient human plasma profiling based on NIST SRM 1950
Project Summary:	Liquid chromatography coupled to high resolution mass spectrometry (LC-HRMS)-based methods have become the gold standard methodology for the comprehensive profiling of the human plasma lipidome. However, both the complexity of lipid chemistry and LC-HRMS-associated data pose challenges to the characterization of this biological matrix. In accordance with the current consensus of quality requirements for LC-HRMS lipidomics data, we aimed to characterize the NIST® Standard Reference Material for Human Plasma (SRM 1950) using an LC-ESI(+/–)-MS method compatible with high-throughput lipidome profiling. We generated a highly curated lipid database with increased coverage, quality, and consistency, including additional quality assurance procedures involving adduct formation, within-method m/z evaluation, retention behavior of species within lipid chain isomers, and expert-driven resolution of isomeric and isobaric interferences. As a proof-of-concept, we showed the utility of our in-house LC-MS lipidomic database –consisting of 592 lipid entries– for the fast, comprehensive, and reliable lipidomic profiling of the human plasma from healthy human volunteers. We are confident that the implementation of this robust resource and methodology will have a significant impact by reducing data redundancy and the current delays and bottlenecks in untargeted plasma lipidomic studies.
Institute:	Universidad CEU San Pablo
Department:	Chemistry and Biochemistry
Laboratory:	CEMBIO
Last Name:	Martínez
First Name:	Sara
Address:	Urbanización Montepríncipe, 28660, Boadilla del Monte, Madrid, Spain
Email:	sara.martinezlopez@ceu.es
Phone:	(+34)913724769

Subject:

Subject ID:	SU003643
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 source	Factor
SA386109	D10P	Plasma	Healthy volunteers
SA386110	D09P	Plasma	Healthy volunteers
SA386111	D08P	Plasma	Healthy volunteers
SA386112	D07P	Plasma	Healthy volunteers
SA386113	D06P	Plasma	Healthy volunteers
SA386114	D05P	Plasma	Healthy volunteers
SA386115	D04P	Plasma	Healthy volunteers
SA386116	D03P	Plasma	Healthy volunteers
SA386117	D02P	Plasma	Healthy volunteers
SA386118	D01P	Plasma	Healthy volunteers
SA386119	NIST_Full Scan_5	Plasma	NIST
SA386120	NIST_Iterative_20ev_2	Plasma	NIST
SA386121	NIST_Iterative_20ev_1	Plasma	NIST
SA386122	NIST_Full Scan_4	Plasma	NIST
SA386123	NIST_Iterative_40eV_3	Plasma	NIST
SA386124	NIST_Full Scan_2	Plasma	NIST
SA386125	NIST_Full Scan_1	Plasma	NIST
SA386126	NIST_Iterative_40eV_5	Plasma	NIST
SA386127	NIST_Full Scan_3	Plasma	NIST
SA386128	NIST_Iterative_40eV_4	Plasma	NIST
SA386129	NIST_Iterative_40eV_2	Plasma	NIST
SA386130	NIST_Iterative_40eV_1	Plasma	NIST
SA386131	NIST_Iterative_20ev_5	Plasma	NIST
SA386132	NIST_Iterative_20ev_4	Plasma	NIST
SA386133	NIST_Iterative_20ev_3	Plasma	NIST
SA386134	Plasma Before Low 2_2-r001	Plasma	NIST_Recovery
SA386135	Plasma Before Low 2_2-r002	Plasma	NIST_Recovery
SA386136	Plasma Before Low 2_3-r001	Plasma	NIST_Recovery
SA386137	Plasma Before Low 2_3-r002	Plasma	NIST_Recovery
SA386138	Plasma Before Med 2_1-r001	Plasma	NIST_Recovery
SA386139	Plasma Before Med 2_3-r002	Plasma	NIST_Recovery
SA386140	Plasma Before Med 2_1-r002	Plasma	NIST_Recovery
SA386141	Plasma Before Med 2_2-r001	Plasma	NIST_Recovery
SA386142	Plasma Before Med 2_2-r002	Plasma	NIST_Recovery
SA386143	Plasma Before Med 2_3-r001	Plasma	NIST_Recovery
SA386144	Plasma Before Low 2_1-r001	Plasma	NIST_Recovery
SA386145	Plasma Before Low 2_1-r002	Plasma	NIST_Recovery
SA386146	Plasma Before High 2_3-r002	Plasma	NIST_Recovery
SA386147	Plasma After High 2_1-r001	Plasma	NIST_Recovery
SA386148	Plasma After Low 2_3-r001	Plasma	NIST_Recovery
SA386149	Plasma After High 2_1-r002	Plasma	NIST_Recovery
SA386150	Plasma After High 2_2-r001	Plasma	NIST_Recovery
SA386151	Plasma After High 2_2-r002	Plasma	NIST_Recovery
SA386152	Plasma After High 2_3-r001	Plasma	NIST_Recovery
SA386153	Plasma After High 2_3-r002	Plasma	NIST_Recovery
SA386154	Plasma After Low 2_1-r001	Plasma	NIST_Recovery
SA386155	Plasma After Low 2_1-r002	Plasma	NIST_Recovery
SA386156	Plasma After Low 2_2-r001	Plasma	NIST_Recovery
SA386157	Plasma After Low 2_2-r002	Plasma	NIST_Recovery
SA386158	Plasma After Low 2_3-r002	Plasma	NIST_Recovery
SA386159	Plasma Before High 2_3-r001	Plasma	NIST_Recovery
SA386160	Plasma After Med 2_1-r001	Plasma	NIST_Recovery
SA386161	Plasma After Med 2_1-r002	Plasma	NIST_Recovery
SA386162	Plasma After Med 2_2-r001	Plasma	NIST_Recovery
SA386163	Plasma After Med 2_2-r002	Plasma	NIST_Recovery
SA386164	Plasma After Med 2_3-r002	Plasma	NIST_Recovery
SA386165	Plasma Before High 2_1-r001	Plasma	NIST_Recovery
SA386166	Plasma Before High 2_1-r002	Plasma	NIST_Recovery
SA386167	Plasma Before High 2_2-r001	Plasma	NIST_Recovery
SA386168	Plasma Before High 2_2-r002	Plasma	NIST_Recovery
SA386169	Plasma After Med 2_3-r001	Plasma	NIST_Recovery

Showing results 1 to 61 of 61

Showing results 1 to 61 of 61

Collection:

Collection ID:	CO003636
Collection Summary:	Sample used is NIST Standard Reference Material (SRM 1950) Metabolites in Human Plasma. Plasma pool was collected from 100 donors in fasting conditions. Plasma was prepared from whole blood that was placed on ice immediately after collection, and lithium heparin was used as the anticoagulant. Each sample was centrifuged at 4°C at 8000 × g for 25 min. Samples were processed and frozen within 60 min from the time of collection.
Sample Type:	Blood (plasma)
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR003652
Treatment Summary:	N/A

Sample Preparation:

Sampleprep ID:	SP003650
Sampleprep Summary:	Lipid extraction protocol involved first, thawing the sample on ice followed by homogenization by vortexing for 2 min. Then, 50 μL of plasma sample was mixed with 800 μL of the solvent mixture containing the ISTD: 2.3 ppm of C17-sphinganine and 4.6 ppm of deuterated (d-31) palmitic acid. In addition, 20 μL of the SPLASH® LIPIDOMIX® were added to the sample. The resulting mixture was vortexed for 20 min at room temperature followed by sample centrifugation at 16,100 x g for 10 min at 15°C. Finally, 300 μL of the resulting supernatant were transferred to LC Chromacol (Thermo Fisher Scientific, Madrid, Spain) vials with insert and centrifuged at 16,100 x g for 5 min at 15°C prior to the analysis. Blank solutions were prepared containing only H2O and the solvent mixture, and the same procedure was followed.

Sampleprep ID:

SP003650

Sampleprep Summary:

Lipid extraction protocol involved first, thawing the sample on ice followed by homogenization by vortexing for 2 min. Then, 50 μL of plasma sample was mixed with 800 μL of the solvent mixture containing the ISTD: 2.3 ppm of C17-sphinganine and 4.6 ppm of deuterated (d-31) palmitic acid. In addition, 20 μL of the SPLASH® LIPIDOMIX® were added to the sample. The resulting mixture was vortexed for 20 min at room temperature followed by sample centrifugation at 16,100 x g for 10 min at 15°C. Finally, 300 μL of the resulting supernatant were transferred to LC Chromacol (Thermo Fisher Scientific, Madrid, Spain) vials with insert and centrifuged at 16,100 x g for 5 min at 15°C prior to the analysis. Blank solutions were prepared containing only H2O and the solvent mixture, and the same procedure was followed.

Combined analysis:

Analysis ID	AN005769	AN005770
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Agilent 1290 Infinity II	Agilent 1290 Infinity II
Column	Agilent InfinityLab Poroshell 120 EC-C18 (100 x 3mm,2.7um)	Agilent InfinityLab Poroshell 120 EC-C18 (100 x 3mm,2.7um)
MS Type	ESI	ESI
MS instrument type	QTOF	QTOF
MS instrument name	Agilent 6545 QTOF	Agilent 6545 QTOF
Ion Mode	POSITIVE	NEGATIVE
Units	Corrected areas	Corrected areas

Chromatography:

Chromatography ID:	CH004377
Chromatography Summary:	RP-UHPLC-ESI(+)-QTOF-MS
Instrument Name:	Agilent 1290 Infinity II
Column Name:	Agilent InfinityLab Poroshell 120 EC-C18 (100 x 3mm,2.7um)
Column Temperature:	50°C
Flow Gradient:	The chromatographic gradient started at 70 % of B at 0 - 1 min, 86 % B at 3.5 - 10 min, 100% B at 11 - 17 min. The starting conditions were recovered by min 17.10, followed by a 1.90 min re-equilibration time, reaching a total running time of 19 min
Flow Rate:	0.6mL/min
Solvent A:	90% Water/10% Methanol; 10 mM Ammonium acetate, 0.2 mM Ammonium fluoride
Solvent B:	20% Acetonitrile/30% Methanol/50% Isopropyl alcohol; 10 mM Ammonium acetate, 0.2 mM Ammonium fluoride
Analytical Time:	19 min
Chromatography Type:	Reversed phase

Chromatography ID:	CH004378
Chromatography Summary:	RP-UHPLC-ESI(-)-QTOF-MS
Instrument Name:	Agilent 1290 Infinity II
Column Name:	Agilent InfinityLab Poroshell 120 EC-C18 (100 x 3mm,2.7um)
Column Temperature:	50°C
Flow Gradient:	The chromatographic gradient started at 70 % of B at 0 - 1 min, 86 % B at 3.5 - 10 min, 100% B at 11 - 17 min. The starting conditions were recovered by min 17.10, followed by a 1.90 min re-equilibration time, reaching a total running time of 19 min
Flow Rate:	0.6mL/min
Solvent A:	90% Water/10% Methanol; 10 mM Ammonium acetate, 0.2 mM Ammonium fluoride
Solvent B:	20% Acetonitrile/30% Methanol/50% Isopropyl alcohol; 10 mM Ammonium acetate, 0.2 mM Ammonium fluoride
Analytical Time:	19 min
Chromatography Type:	Reversed phase

MS:

MS ID:	MS005489
Analysis ID:	AN005769
Instrument Name:	Agilent 6545 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	The Agilent 6545 QTOF-MS equipped with a AJS ESI ion source was set with the following parameters: 175 V fragmentor, 65 V skimmer, 3500 V capillary voltage, 750 V octupole radio frequency voltage, 11 L/min nebulizer gas flow, 290°C gas temperature, 40 psi nebulizer gas pressure, 11 L/min sheath gas flow, and 370 °C sheath gas temperature. The mass spectrometer operated in full scan mode, scanning from m/z 40 - 1700 at a scan rate of 3 spectra/s. During the analysis, a solution containing two reference mass compounds was continuously infused to the system at a flow rate of 1 mL/min to provide mass correction. The reference masses used were m/z 121.0509 (purine detected as [C5H4N4 + H]+) and m/z 922.0098 (HP-0921 detected as [C18H18O6N3P3F24 + H]+) for ESI(+) and m/z 119.0363 (purine detected as [C5H4N4 - H]-) and m/z 1033.9881 (HP-0921 detected as [C18H18O6N3P3F24 + CF3COOH-H]-) for ESI(–). At the end of the analysis, ten iterative-MS/MS runs were performed for both, positive and negative ionization modes using a QC sample. They were operated with a MS and MS/MS scan rates of 3 spectra/s, 3 precursors per cycle, a mass range of m/z 40 - 1700, a narrow (~ 1.3 amu) MS/MS isolation width, and 5000 counts and 0.001 % of MS/MS threshold. The collision energy for the first five iterative-MS/MS runs was set at 20 eV, and the subsequent five runs were performed at 40 eV. To ensure accuracy, reference masses and contaminants detected in blank samples were excluded from the analysis. This prevented thein inclusion in the iterative-MS/MS runs. Data was acquired using MassHunter Workstation Software LC-MS Data Acquisition v B.09.00 (Agilent Technologies, Waldbronn, Germany).
Ion Mode:	POSITIVE

MS ID:	MS005490
Analysis ID:	AN005770
Instrument Name:	Agilent 6545 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	The Agilent 6545 QTOF-MS equipped with a AJS ESI ion source was set with the following parameters: 175 V fragmentor, 65 V skimmer, 3500 V capillary voltage, 750 V octopole radio frequency voltage, 11 L/min nebulizer gas flow, 290 °C gas temperature, 40 psi nebulizer gas pressure, 11 L/min sheath gas flow, and 370 °C sheath gas temperature. The mass spectrometer operated in full scan mode, scanning from m/z 40 - 1700 at a scan rate of 3 spectra/s. During the analysis, a solution containing two reference mass compounds was continuously infused to the system at a flow rate of 1 mL/min to provide mass correction. The reference masses used were m/z 121.0509 (purine detected as [C5H4N4 + H]+) and m/z 922.0098 (HP-0921 detected as [C18H18O6N3P3F24 + H]+) for ESI(+) and m/z 119.0363 (purine detected as [C5H4N4 - H]-) and m/z 1033.9881 (HP-0921 detected as [C18H18O6N3P3F24 + CF3COOH-H]-) for ESI(–). At the end of the analysis, ten iterative-MS/MS runs were performed for both, positive and negative ionization modes using a QC sample. They were operated with a MS and MS/MS scan rates of 3 spectra/s, 3 precursors per cycle, a mass range of m/z 40 - 1700, a narrow (~ 1.3 amu) MS/MS isolation width, and 5000 counts and 0.001 % of MS/MS threshold. The collision energy for the first five iterative-MS/MS runs was set at 20 eV, and the subsequent five runs were performed at 40 eV. To ensure accuracy, reference masses and contaminants detected in blank samples were excluded from the analysis. This prevented thein inclusion in the iterative-MS/MS runs. Data was acquired using MassHunter Workstation Software LC-MS Data Acquisition v B.09.00 (Agilent Technologies, Waldbronn, Germany).
Ion Mode:	NEGATIVE