Summary of Study ST001493

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 PR001011. The data can be accessed directly via it's Project DOI: 10.21228/M8111X 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	ST001493
Study Title	Dynamic binning peak detection and assessment of various lipidomics liquid chromatography-mass spectrometry pre-processing platforms
Study Summary	Liquid chromatography-mass spectrometry (LC-MS) based lipidomics generate a large dataset, which requires high-performance data pre-processing tools for their interpretation such as XCMS, mzMine and Progenesis. These pre-processing tools rely heavily on accurate peak detection, which depends on setting the peak detection mass tolerance (PDMT) properly. The PDMT is usually set with a fixed value in either ppm or Da units. However, this fixed value may result in duplicates or missed peak detection. Therefore, we developed the dynamic binning method for accurate peak detection, which takes into account the peak broadening described by well-known physics laws of ion separation and set dynamically the value of PDMT as a function of m/z. Namely, in our method, the PDMT is proportional to for FTICR, to for Orbitrap, to m/z for Q-TOF and is a constant for Quadrupole mass analyzer, respectively. The dynamic binning method was implemented in XCMS. Our further goal was to compare the performance of different lipidomics pre-processing tools to find differential compounds. We have generated set samples with 43 lipids internal standards differentially spiked to aliquots of one human plasma lipid sample using Orbitrap LC-MS/MS. The performance of the various pipelines using aligned parameter sets was quantified by a quality score system which reflects the ability of a pre-processing pipeline to detect differential peaks spiked at various concentration levels. The quality score indicates that the dynamic binning method improves the performance of XCMS (maximum p-value 9.8·10-3 of two-sample Wilcoxon test). The modified XCMS software was further compared with mzMine and Progenesis. The results showed that modified XCMS and Progenesis had a similarly good performance in the aspect of finding differential compounds. In addition, Progenesis shows lower variability as indicated by lower CVs, followed by XCMS and mzMine. The lower variability of Progenesis improve the quantification, however, provide an incorrect quantification abundance order of spiked-in internal standards.
Institute	University of Groningen
Last Name	Péter
First Name	Horvatovich
Address	Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
Email	p.l.horvatovich@rug.nl
Phone	+31 (0)50 363 3341
Submit Date	2020-09-25
Num Groups	6
Total Subjects	1
Study Comments	Different concentrations of lipid standard mixture were added to the plasma lipid extract aliquots
Publications	Under review
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2020-10-13
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001011
Project DOI:	doi: 10.21228/M8111X
Project Title:	Dynamic binning
Project Type:	MS analysis
Project Summary:	Using dynamic binning theory to improve the peak detection in LC-MS based lipidomics
Institute:	University of Groningen
Department:	Department of Analytical Biochemistry
Last Name:	Horvatovich
First Name:	Péter
Address:	Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
Email:	p.l.horvatovich@rug.nl
Phone:	+31 (0)50 363 3341
Funding Source:	China Scholarship Council grant No. 201708500094. This research was part of the Netherlands X-omics Initiative and partially funded by NWO, project 184.034.019.
Publications:	Under review

Subject:

Subject ID:	SU001567
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606

Factors:

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

mb_sample_id	local_sample_id	Treatment
SA125872	PlasmaIS1_59	Plasma + IS 1
SA125873	PlasmaIS1_66	Plasma + IS 1
SA125874	PlasmaIS1_73	Plasma + IS 1
SA125875	PlasmaIS1_45	Plasma + IS 1
SA125876	PlasmaIS1_80	Plasma + IS 1
SA125877	PlasmaIS1_52	Plasma + IS 1
SA125878	PlasmaIS1_16	Plasma + IS 1
SA125879	PlasmaIS1_30	Plasma + IS 1
SA125880	PlasmaIS1_23	Plasma + IS 1
SA125881	PlasmaIS1_38	Plasma + IS 1
SA125882	PlasmaIS1-16_34	Plasma + IS 1/16
SA125883	PlasmaIS1-16_19	Plasma + IS 1/16
SA125884	PlasmaIS1-16_12	Plasma + IS 1/16
SA125885	PlasmaIS1-16_41	Plasma + IS 1/16
SA125886	PlasmaIS1-16_26	Plasma + IS 1/16
SA125887	PlasmaIS1-16_76	Plasma + IS 1/16
SA125888	PlasmaIS1-16_48	Plasma + IS 1/16
SA125889	PlasmaIS1-16_62	Plasma + IS 1/16
SA125890	PlasmaIS1-16_69	Plasma + IS 1/16
SA125891	PlasmaIS1-16_55	Plasma + IS 1/16
SA125892	PlasmaIS1-2_79	Plasma + IS 1/2
SA125893	PlasmaIS1-2_58	Plasma + IS 1/2
SA125894	PlasmaIS1-2_72	Plasma + IS 1/2
SA125895	PlasmaIS1-2_51	Plasma + IS 1/2
SA125896	PlasmaIS1-2_65	Plasma + IS 1/2
SA125897	PlasmaIS1-2_37	Plasma + IS 1/2
SA125898	PlasmaIS1-2_44	Plasma + IS 1/2
SA125899	PlasmaIS1-2_22	Plasma + IS 1/2
SA125900	PlasmaIS1-2_15	Plasma + IS 1/2
SA125901	PlasmaIS1-2_29	Plasma + IS 1/2
SA125902	PlasmaIS1-4_28	Plasma + IS 1/4
SA125903	PlasmaIS1-4_21	Plasma + IS 1/4
SA125904	PlasmaIS1-4_14	Plasma + IS 1/4
SA125905	PlasmaIS1-4_36	Plasma + IS 1/4
SA125906	PlasmaIS1-4_78	Plasma + IS 1/4
SA125907	PlasmaIS1-4_43	Plasma + IS 1/4
SA125908	PlasmaIS1-4_64	Plasma + IS 1/4
SA125909	PlasmaIS1-4_71	Plasma + IS 1/4
SA125910	PlasmaIS1-4_57	Plasma + IS 1/4
SA125911	PlasmaIS1-4_50	Plasma + IS 1/4
SA125912	PlasmaIS1-8_49	Plasma + IS 1/8
SA125913	PlasmaIS1-8_63	Plasma + IS 1/8
SA125914	PlasmaIS1-8_70	Plasma + IS 1/8
SA125915	PlasmaIS1-8_42	Plasma + IS 1/8
SA125916	PlasmaIS1-8_77	Plasma + IS 1/8
SA125917	PlasmaIS1-8_56	Plasma + IS 1/8
SA125918	PlasmaIS1-8_13	Plasma + IS 1/8
SA125919	PlasmaIS1-8_35	Plasma + IS 1/8
SA125920	PlasmaIS1-8_20	Plasma + IS 1/8
SA125921	PlasmaIS1-8_27	Plasma + IS 1/8
SA125922	PlasmaIS0_54	Pure Plasma
SA125923	PlasmaIS0_47	Pure Plasma
SA125924	PlasmaIS0_68	Pure Plasma
SA125925	PlasmaIS0_40	Pure Plasma
SA125926	PlasmaIS0_61	Pure Plasma
SA125927	PlasmaIS0_18	Pure Plasma
SA125928	PlasmaIS0_75	Pure Plasma
SA125929	PlasmaIS0_11	Pure Plasma
SA125930	PlasmaIS0_25	Pure Plasma
SA125931	PlasmaIS0_33	Pure Plasma

Showing results 1 to 60 of 60

Showing results 1 to 60 of 60

Collection:

Collection ID:	CO001562
Collection Summary:	LC-MS grade acetonitrile (ACN), methanol (MeOH), isopropanol (IPA) and chloroform were purchased from Biosolve BV (Valkenswaard, The Netherlands). Ammonium formate (AmF), formic acid (FA) and tert-Butyl methyl ether (MTBE) were purchased from Sigma Aldrich (St. Louis, MO). Various lipid standards were purchased from Avanti Polar Lipids, Inc. (Alabaster, AL). Heparin-anticoagulated plasma samples were obtained from adult patients at the University Medical Center Groningen (UMCG) in an anonymous manner and were combined to generate a standard plasma sample.
Sample Type:	Blood (plasma)
Collection Method:	Anonymous
Collection Location:	University Medical Center Groningen (UMCG)

Treatment:

Treatment ID:	TR001582
Treatment Summary:	60 µl of plasma was mixed with 300 µl of MeOH and sonicate for 10 min. Subsequently, 1000 µl MTBE was added and the mixture was kept under 25 °C on a shaker (900 rpm) for 30 min. Phase separation was induced by adding 190 µl ultrapure water. Then the mixture was centrifuged at 3000 RCF for 10 min and the 850 µl upper phase were transferred to a new tube. The re-extraction was performed by adding 600 µl MTBE/MeOH/ultrapure water (10:3:2.5, v/v/v) into the lower phase and 500 µl were collected after centrifugation to combine with the previous organic phase. The combined lipid extract solution was aliquoted into 6 tubes (190 µl per tube) to generate plasma lipid matrix. Different concentrations of lipid standard mixture were added to the plasma lipid extract aliquots and dried in a vacuum centrifuge under 45 °C. The dried lipid extracts were resuspended with 30 µl chloroform:MeOH:MQ (60:30:4.5, v/v/v) and further diluted with 90 µl (IPA:ACN:MQ 2:1:1 v/v/v) for LC-MS analysis.

Treatment ID:

TR001582

Treatment Summary:

60 µl of plasma was mixed with 300 µl of MeOH and sonicate for 10 min. Subsequently, 1000 µl MTBE was added and the mixture was kept under 25 °C on a shaker (900 rpm) for 30 min. Phase separation was induced by adding 190 µl ultrapure water. Then the mixture was centrifuged at 3000 RCF for 10 min and the 850 µl upper phase were transferred to a new tube. The re-extraction was performed by adding 600 µl MTBE/MeOH/ultrapure water (10:3:2.5, v/v/v) into the lower phase and 500 µl were collected after centrifugation to combine with the previous organic phase. The combined lipid extract solution was aliquoted into 6 tubes (190 µl per tube) to generate plasma lipid matrix. Different concentrations of lipid standard mixture were added to the plasma lipid extract aliquots and dried in a vacuum centrifuge under 45 °C. The dried lipid extracts were resuspended with 30 µl chloroform:MeOH:MQ (60:30:4.5, v/v/v) and further diluted with 90 µl (IPA:ACN:MQ 2:1:1 v/v/v) for LC-MS analysis.

Sample Preparation:

Sampleprep ID:	SP001575
Sampleprep Summary:	20 different deuterium-labelled lipid IS and 4 deuterium-labelled lipid IS premix were selected to cover the major lipid classes and distributed evenly in mz and retention time range. All lipid standard stock solutions were diluted with chloroform: MeOH (1:1, v/v) and mixed to generate a lipid IS mixture with optimized concentrations for each standard to acquire adequate signal intensity. The lipid IS mixture was used to create a dilution series where concentration ratios were set to a factor of two starting from concentration 1 up to concentration 1/16.

Sampleprep ID:

SP001575

Sampleprep Summary:

20 different deuterium-labelled lipid IS and 4 deuterium-labelled lipid IS premix were selected to cover the major lipid classes and distributed evenly in mz and retention time range. All lipid standard stock solutions were diluted with chloroform: MeOH (1:1, v/v) and mixed to generate a lipid IS mixture with optimized concentrations for each standard to acquire adequate signal intensity. The lipid IS mixture was used to create a dilution series where concentration ratios were set to a factor of two starting from concentration 1 up to concentration 1/16.

Combined analysis:

Analysis ID	AN002475
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	Waters Acquity
Column	Waters Acquity CSH C18 (100 x 2.1mm,1.7um)
MS Type	ESI
MS instrument type	Orbitrap
MS instrument name	Thermo Q Exactive Orbitrap
Ion Mode	POSITIVE
Units	Peak area

Chromatography:

Chromatography ID:	CH001813
Chromatography Summary:	LC-MS lipid analysis was performed on an Ultimate 3000 High-Performance UPLC. Chromatography separation was achieved with an Acquity UPLC CSH column [1.7 μm, 100 × 2.1 mm, (Waters Corporation, Milford, MA)] under 55°C with a flow rate of 0.4 ml/min. Mobile phase A was composed of ultrapure water/acetonitrile 40:60 (v/v), 10 mM ammonium formate and 0.1% formic acid. Mobile phase B contained ACN/IPA 10:90 (v/v) with 10 mM ammonium formate and 0.1% formic acid. The LC gradient started with 40% mobile phase B and raised to 43% mobile phase B in 2 min. The percentage of mobile phase B raised to 50% in the next 0.1 min and increased to 54% in next 9.9 min. Mobile phase B raised to 70% in 0.1 min and increased to 99% in 5.9 min and maintained at 99% for 1 min. Then the percentage of mobile phase B went back to 40% in 0.1 min and the system was equilibrated for 3.9 min before the next run started.
Instrument Name:	Waters Acquity
Column Name:	Waters Acquity CSH C18 (100 x 2.1mm,1.7um)
Column Temperature:	under 55°C
Flow Rate:	0.4 ml/min
Solvent A:	40% water/60% acetonitrile; 0.1% formic acid; 10 mM ammonium formate
Solvent B:	10% acetonitrile/90% isopropanol; 0.1% formic acid; 10 mM ammonium formate
Chromatography Type:	Reversed phase

MS:

MS ID:	MS002295
Analysis ID:	AN002475
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	The MS was set for positive mode and data-dependent acquisition. A full MS scan the range from 250-1750 Da was acquired at resolution 70,000 FWHM at 200 Da. (AGC target was set to 1·106, maximum injection time was 50 ms, MS1 scan was followed by up to 8 MS/MS events with a collision energy of 25 eV at resolution 17,500 FWHM at 200 Da. The precursor isolation window was set to 1.5 Da with the dynamic exclusion time of 6 s. The ionization settings were as follows: capillary voltage, +3.2 kV; capillary temperature: 320 °C; sheath gas/auxiliary gas: 60/20.
Ion Mode:	POSITIVE