Optimization of a liquid chromatography-ion mobility-high resolution mass spectrometry platform for untargeted lipidomics and application to HepaRG cell extracts

Silva, Katyeny Manuela da; Iturrospe, Elias; Heyrman, Joris; Koelmel, Jeremy P.; Cuykx, Matthias; Vanhaecke, Tamara; Nuijs, Alexander L.N. van

doi:10.1016/j.talanta.2021.122808

Cited by 21 publications

(18 citation statements)

References 108 publications

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“…increasing number of curated and freely available CCS databases [15][16][17] has popularized the use of CCS values as an identification parameter intended for standard-free identification workflows [17][18][19].…”

Section: Introductionmentioning

confidence: 99%

“…As a derived property, the collision cross section ( CCS ) of an ion can be calculated with excellent interlaboratory precisions of typically in the range of 1–2% reported in several studies [ 12 – 14 ]. Moreover, the increasing number of curated and freely available CCS databases [ 15 – 17 ] has popularized the use of CCS values as an identification parameter intended for standard-free identification workflows [ 17 – 19 ].…”

Section: Introductionmentioning

confidence: 99%

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Critical evaluation of the role of external calibration strategies for IM-MS

et al. 2022

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The major benefits of integrating ion mobility (IM) into LC–MS methods for small molecules are the additional separation dimension and especially the use of IM-derived collision cross sections (CCS) as an additional ion-specific identification parameter. Several large CCS databases are now available, but outliers in experimental interplatform IM-MS comparisons are identified as a critical issue for routine use of CCS databases for identity confirmation. We postulate that different routine external calibration strategies applied for traveling wave (TWIM-MS) in comparison to drift tube (DTIM-MS) and trapped ion mobility (TIM-MS) instruments is a critical factor affecting interplatform comparability. In this study, different external calibration approaches for IM-MS were experimentally evaluated for 87 steroids, for which TWCCSN2, DTCCSN2 and TIMCCSN2 are available. New reference CCSN2 values for commercially available and class-specific calibrant sets were established using DTIM-MS and the benefit of using consolidated reference values on comparability of CCSN2 values assessed. Furthermore, use of a new internal correction strategy based on stable isotope labelled (SIL) internal standards was shown to have potential for reducing systematic error in routine methods. After reducing bias for CCSN2 between different platforms using new reference values (95% of TWCCSN2 values fell within 1.29% of DTCCSN2 and 1.12% of TIMCCSN2 values, respectively), remaining outliers could be confidently classified and further studied using DFT calculations and CCSN2 predictions. Despite large uncertainties for in silico CCSN2 predictions, discrepancies in observed CCSN2 values across different IM-MS platforms as well as non-uniform arrival time distributions could be partly rationalized.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Critical evaluation of the role of external calibration strategies for IM-MS

et al. 2022

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“…Surprisingly, when making the same comparison in complex samples like HepaRG cell extracts, there was no signal intensity gain for most lipids in multiplexing mode. Nonetheless, lipidomics analysis in complex samples can still benefit from multiplexing in means of detector saturation and noise reduction that can increase peak deconvolution, feature finding and as a result provide a more confident lipid annotation, especially of low abundant lipids such as oxylipins [37].…”

Section: Scan Modementioning

confidence: 99%

Recent developments in data acquisition, treatment and analysis with ion mobility‐mass spectrometry for lipidomics

et al. 2022

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Lipids are involved in many biological processes and their study is constantly increasing. To identify a lipid among thousand requires of reliable methods and techniques. Ion Mobility (IM) can be coupled with Mass Spectrometry (MS) to increase analytical selectivity in lipid analysis of lipids. IM-MS has experienced an enormous development in several aspects, including instrumentation, sensitivity, amount of information collected and lipid identification capabilities. This review summarizes the latest developments in IM-MS analyses for lipidomics and focuses on the current acquisition modes in IM-MS, the approaches for the pre-treatment of the acquired data and the subsequent data analysis. Methods and tools for the calculation of Collision Cross Section (CCS) values of analytes are also reviewed. CCS values are commonly studied to support the identification of lipids, providing a quasi-orthogonal property that increases the confidence level in the annotation of compounds and can be matched in CCS databases. The information contained in this review might be of help to new users of IM-MS to decide the adequate instrumentation and software to perform IM-MS experiments for lipid analyses, but also for other experienced researchers that can reconsider their routines and protocols.

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“…Analytical measurements were performed on an Agilent 1290 Infinity II LC system coupled to an Agilent 6560 drift tube-ion mobility-quadrupole-time-of-flight high-resolution mass spectrometer (DTIM-QToF-HRMS) (Agilent Technologies, Santa Clara, USA) using Agilent Dual Jet Stream Electrospray Ionization (ESI) in positive (+) and negative modes (−), as previously described [15]. Data were acquired in 2 GHz extended dynamic mode with a scan range of 100-1700 m/z in profile mode.…”

Section: Instrumental Analysismentioning

confidence: 99%

“…Qualitative information on lipid composition that can be used for further quantitative measurements to study metabolic diseases and exposure to toxicants is of special interest since this information is still scarce [1]. In this study, an analytical workflow for zebrafish liver tissues was explored using an untargeted RPLC-HRMS-based platform previously applied for liver cell extracts [15]. Different mixtures of organic solvents were tested for lipid extraction: in house extraction (HE) method (modified Bligh-Dyer [16]) consisting of methanol (MeOH)/chloroform (CHCl 3 )/water (H 2 O) (3/2/2, v/v/v) and previously optimized for the HepaRG liver cell line [17,18], a modified in house extraction (MHE) method consisting of MeOH/dichloromethane (CH 2 Cl 2 )/H 2 O (2/3/2, v/v/v) and the Matyash et al [19] extraction (ME) using MeOH/methyl-tert-butyl ether (MTBE)/H 2 O (3/10/2.5, v/v/v).…”

mentioning

confidence: 99%

Lipidomics profiling of zebrafish liver through untargeted liquid chromatography‐high resolution mass spectrometry

Silva

Iturrospe

Boom

et al. 2022

J of Separation Science

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Lipidomics analysis of zebrafish tissues has shown promising results to understand disease‐related outcomes of exposure to toxic substances at a molecular level. However, knowledge about their lipidome is limited, as most untargeted studies only identify the lipids that are statistically significant in their setup. In this work, liquid chromatography‐high resolution mass spectrometry was used to study different aspects of the analytical workflow, that is, extraction solvents (methanol/chloroform/water (3/2/2, v/v/v), methanol/dichloromethane/water (2/3/2, v/v/v) and methanol/methyl‐tert‐butyl ether/water (3/10/2.5, v/v/v), instrumental response, and strategies used for lipid annotation. The number of high‐quality features (relative standard deviation of the intensity values ≤ 10% in the range 103−107 counts) was affected by the dilution of lipid extracts, indicating that it is an important parameter for developing untargeted methods. The workflows used allowed the selection of a dilution factor to annotate 712 lipid species (507 bulk lipids) in zebrafish liver using four software (LipidMatch, LipidHunter, MS‐DIAL, and Lipostar). Retention time mapping was a valuable tool to filter lipid annotations obtained from automatic software annotations. The lipid profiling of zebrafish livers will help in a better understanding of the true constitution of their lipidome at the species level, as well as in the use of zebrafish in toxicological studies.

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Optimization of a liquid chromatography-ion mobility-high resolution mass spectrometry platform for untargeted lipidomics and application to HepaRG cell extracts

Cited by 21 publications

References 108 publications

Critical evaluation of the role of external calibration strategies for IM-MS

Critical evaluation of the role of external calibration strategies for IM-MS

Recent developments in data acquisition, treatment and analysis with ion mobility‐mass spectrometry for lipidomics

Lipidomics profiling of zebrafish liver through untargeted liquid chromatography‐high resolution mass spectrometry

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