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:

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.