Summary of study ST001493

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, 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.


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Study IDST001493
Study TitleDynamic binning peak detection and assessment of various lipidomics liquid chromatography-mass spectrometry pre-processing platforms
Study SummaryLiquid 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.
University of Groningen
Last NamePéter
First NameHorvatovich
AddressAntonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
Phone+31 (0)50 363 3341
Submit Date2020-09-25
Num Groups6
Total Subjects1
Study CommentsDifferent concentrations of lipid standard mixture were added to the plasma lipid extract aliquots
PublicationsUnder review
Raw Data AvailableYes
Raw Data File Type(s).mzML
Analysis Type DetailOther
Release Date2020-10-13
Release Version1
Horvatovich Péter Horvatovich Péter application/zip

Select appropriate tab below to view additional metadata details:


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


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

mb_sample_id local_sample_id Treatment
SA125872PlasmaIS1_59Plasma + IS 1
SA125873PlasmaIS1_66Plasma + IS 1
SA125874PlasmaIS1_73Plasma + IS 1
SA125875PlasmaIS1_45Plasma + IS 1
SA125876PlasmaIS1_80Plasma + IS 1
SA125877PlasmaIS1_52Plasma + IS 1
SA125878PlasmaIS1_16Plasma + IS 1
SA125879PlasmaIS1_30Plasma + IS 1
SA125880PlasmaIS1_23Plasma + IS 1
SA125881PlasmaIS1_38Plasma + IS 1
SA125882PlasmaIS1-16_34Plasma + IS 1/16
SA125883PlasmaIS1-16_19Plasma + IS 1/16
SA125884PlasmaIS1-16_12Plasma + IS 1/16
SA125885PlasmaIS1-16_41Plasma + IS 1/16
SA125886PlasmaIS1-16_26Plasma + IS 1/16
SA125887PlasmaIS1-16_76Plasma + IS 1/16
SA125888PlasmaIS1-16_48Plasma + IS 1/16
SA125889PlasmaIS1-16_62Plasma + IS 1/16
SA125890PlasmaIS1-16_69Plasma + IS 1/16
SA125891PlasmaIS1-16_55Plasma + IS 1/16
SA125892PlasmaIS1-2_79Plasma + IS 1/2
SA125893PlasmaIS1-2_58Plasma + IS 1/2
SA125894PlasmaIS1-2_72Plasma + IS 1/2
SA125895PlasmaIS1-2_51Plasma + IS 1/2
SA125896PlasmaIS1-2_65Plasma + IS 1/2
SA125897PlasmaIS1-2_37Plasma + IS 1/2
SA125898PlasmaIS1-2_44Plasma + IS 1/2
SA125899PlasmaIS1-2_22Plasma + IS 1/2
SA125900PlasmaIS1-2_15Plasma + IS 1/2
SA125901PlasmaIS1-2_29Plasma + IS 1/2
SA125902PlasmaIS1-4_28Plasma + IS 1/4
SA125903PlasmaIS1-4_21Plasma + IS 1/4
SA125904PlasmaIS1-4_14Plasma + IS 1/4
SA125905PlasmaIS1-4_36Plasma + IS 1/4
SA125906PlasmaIS1-4_78Plasma + IS 1/4
SA125907PlasmaIS1-4_43Plasma + IS 1/4
SA125908PlasmaIS1-4_64Plasma + IS 1/4
SA125909PlasmaIS1-4_71Plasma + IS 1/4
SA125910PlasmaIS1-4_57Plasma + IS 1/4
SA125911PlasmaIS1-4_50Plasma + IS 1/4
SA125912PlasmaIS1-8_49Plasma + IS 1/8
SA125913PlasmaIS1-8_63Plasma + IS 1/8
SA125914PlasmaIS1-8_70Plasma + IS 1/8
SA125915PlasmaIS1-8_42Plasma + IS 1/8
SA125916PlasmaIS1-8_77Plasma + IS 1/8
SA125917PlasmaIS1-8_56Plasma + IS 1/8
SA125918PlasmaIS1-8_13Plasma + IS 1/8
SA125919PlasmaIS1-8_35Plasma + IS 1/8
SA125920PlasmaIS1-8_20Plasma + IS 1/8
SA125921PlasmaIS1-8_27Plasma + IS 1/8
SA125922PlasmaIS0_54Pure Plasma
SA125923PlasmaIS0_47Pure Plasma
SA125924PlasmaIS0_68Pure Plasma
SA125925PlasmaIS0_40Pure Plasma
SA125926PlasmaIS0_61Pure Plasma
SA125927PlasmaIS0_18Pure Plasma
SA125928PlasmaIS0_75Pure Plasma
SA125929PlasmaIS0_11Pure Plasma
SA125930PlasmaIS0_25Pure Plasma
SA125931PlasmaIS0_33Pure Plasma
Showing results 1 to 60 of 60


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 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.

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 instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Units Peak area


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:ultrapure water/acetonitrile 40:60 (v/v), 10 mM ammonium formate and 0.1% formic acid
Solvent B:ACN/IPA 10:90 (v/v) with 10 mM ammonium formate and 0.1% formic acid
Chromatography Type:Reversed phase


MS ID:MS002295
Analysis ID:AN002475
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
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.