1
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Ventura G, Calvano CD, Bianco M, Castellaneta A, Losito I, Cataldi TRI. PE, or not PE, that is the question: The case of overlooked lyso-N-acylphosphatidylethanolamines. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9527. [PMID: 37117037 DOI: 10.1002/rcm.9527] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/18/2023] [Accepted: 04/24/2023] [Indexed: 06/17/2023]
Abstract
RATIONALE Lyso derivatives of N-acyl-1,2-diacylglycero-3-phosphoethanolamines (L-NAPEs) are a lipid class mostly expressed in vegetables during stress and tissue damage that is involved in the synthesis of the lipid mediator N-acylethanolamines. L-NAPEs can be challenging to distinguish from isomeric phosphatidylethanolamines (PEs), especially in extracted complex samples where they could be confused with abundant PEs. METHODS In this study, hydrophilic interaction liquid chromatography with electrospray ionization hyphenated with (tandem) mass spectrometry (MS) was proposed to distinguish L-NAPEs and PEs as deprotonated molecules, [M - H]─ , using both high-resolution/accuracy Fourier transform MS and low-resolution linear ion trap (LIT) mass analyzers. MS3 experiments of [M - H - KE]─ as precursor ions (KE, ketene loss) using the LIT instrument allowed us to distinguish between isomeric L-NAPE and PE species. RESULTS Regiochemical rules were proposed working on enzymatically synthesized L-NAPEs. A few key differences in MS/MS spectra, including abnormal intensity of acyl chain losses as fatty acids, the presence of N-acylphosphoethanolamine ions, and diagnostic ions of the polar head, were disclosed. Additionally, MS3 spectra of [M - H - KE]─ as precursor ions allowed us to confirm the identification of L-NAPE species. The proposed rules were applied to samples extracted from tomato by-products including stems and leaves. CONCLUSIONS Overall, our methodology is demonstrated as a robust approach to recognizing L-NAPEs in complex samples. L-NAPEs 18:2-N-18:2, 18:2-N-18:3, 18:3-N-18:2, and 18:2-N-18:1 were the prevailing compounds in the analyzed tomato samples, accounting for more than 90%. In summary, a reliable method for identifying L-NAPEs in complex samples is described. The proposed method could prevent overlooking L-NAPEs and overestimating isomeric PE species in future lipid analyses.
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Affiliation(s)
- Giovanni Ventura
- Department of Chemistry, University of Bari Aldo Moro, Bari, Italy
- Interdepartmental Research Center SMART, University of Bari Aldo Moro, Bari, Italy
| | - Cosima Damiana Calvano
- Department of Chemistry, University of Bari Aldo Moro, Bari, Italy
- Interdepartmental Research Center SMART, University of Bari Aldo Moro, Bari, Italy
| | | | | | - Ilario Losito
- Department of Chemistry, University of Bari Aldo Moro, Bari, Italy
- Interdepartmental Research Center SMART, University of Bari Aldo Moro, Bari, Italy
| | - Tommaso R I Cataldi
- Department of Chemistry, University of Bari Aldo Moro, Bari, Italy
- Interdepartmental Research Center SMART, University of Bari Aldo Moro, Bari, Italy
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2
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Züllig T, Köfeler HC. HIGH RESOLUTION MASS SPECTROMETRY IN LIPIDOMICS. MASS SPECTROMETRY REVIEWS 2021; 40:162-176. [PMID: 32233039 PMCID: PMC8049033 DOI: 10.1002/mas.21627] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 03/06/2020] [Indexed: 05/04/2023]
Abstract
The boost of research output in lipidomics during the last decade is tightly linked to improved instrumentation in mass spectrometry. Associated with this trend is the shift from low resolution-toward high-resolution lipidomics platforms. This review article summarizes the state of the art in the lipidomics field with a particular focus on the merits of high mass resolution. Following some theoretical considerations on the benefits of high mass resolution in lipidomics, it starts with a historical perspective on lipid analysis by sector instruments and moves further to today's instrumental approaches, including shotgun lipidomics, liquid chromatography-mass spectrometry, matrix-assisted laser desorption ionization-time-of-flight, and imaging lipidomics. Subsequently, several data processing and data analysis software packages are critically evaluated with all their pros and cons. Finally, this article emphasizes the importance and necessity of quality standards as the field evolves from its pioneering phase into a mature and robust omics technology and lists various initiatives for improving the applicability of lipidomics. © 2020 The Authors. Mass Spectrometry Reviews published by John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Thomas Züllig
- Core Facility Mass SpectrometryMedical University of Graz, ZMFGrazAustria
| | - Harald C. Köfeler
- Core Facility Mass SpectrometryMedical University of Graz, ZMFGrazAustria
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3
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Castellaneta A, Losito I, Coniglio D, Leoni B, Santamaria P, Di Noia MA, Palmieri L, Calvano CD, Cataldi TRI. LIPIC: An Automated Workflow to Account for Isotopologue-Related Interferences in Electrospray Ionization High-Resolution Mass Spectra of Phospholipids. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1008-1019. [PMID: 33705659 DOI: 10.1021/jasms.1c00008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In the past decade, hydrophilic interaction liquid chromatography (HILIC) has emerged as an efficient alternative to reversed-phase chromatography (RPC) for the analysis of phospholipid (PL) mixtures based on mass spectrometric detection. Since the separation of PL by HILIC is chiefly based on their headgroup, the mass spectrum of each class can be obtained by spectral averaging under the corresponding HILIC band. Using experimental m/z values resulting from high mass resolution/accuracy instruments, the sum compositions of PL in a specific class can be thus inferred but partial overlapping may occur between signals related to the M + 0 isotopologue of one species and the M + 2/M + 4 isotopologues of species having one/two more C═C bonds in their chemical structures. Here, an automated workflow, named LIPIC (lipid isotopic pattern interference correction), is proposed to account for such interferences. Starting from the experimentally verified assumption that peaks in isotope patterns are Gaussian, LIPIC predicts, as a function of m/z ratio, signal intensities due to M + 2 and M + 4 isotopologues of species with one or two more C = C bonds than the target one and calculates the corrected intensity for the M + 0 isotopologue of the latter. Thanks to an iterative procedure, the suggested algorithm compensates also for slight shifts occurring between experimental and theoretical m/z ratios related to isotopologue peaks. Examples of applications to simulated and experimental mass spectra of two PL classes, i.e., phosphatidylcholines (PC) and cardiolipins (CL), emphasize the increased extent of correction at the increase of molecular masses of involved species.
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4
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Höring M, Ejsing CS, Krautbauer S, Ertl VM, Burkhardt R, Liebisch G. Accurate quantification of lipid species affected by isobaric overlap in Fourier-transform mass spectrometry. J Lipid Res 2021; 62:100050. [PMID: 33600775 PMCID: PMC8010702 DOI: 10.1016/j.jlr.2021.100050] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/21/2021] [Accepted: 02/05/2021] [Indexed: 11/05/2022] Open
Abstract
Lipidomics data require consideration of ions with near-identical masses, which comprises among others the Type-II isotopic overlap. This overlap occurs in series of lipid species differing only by number of double bonds (DBs) mainly because of the natural abundance of 13C-atoms. High-resolution mass spectrometry, such as Fourier-transform mass spectrometry (FTMS), is capable of resolving Type-II overlap depending on mass resolving power. In this work, we evaluated FTMS quantification accuracy of lipid species affected by Type-II overlap. Spike experiments with lipid species pairs of various lipid classes were analyzed by flow injection analysis-FTMS. Accuracy of quantification was evaluated without and with Type-II correction (using relative isotope abundance) as well as utilizing the first isotopic peak (M+1). Isobaric peaks, which were sufficiently resolved, were most accurate without Type-II correction. In cases of partially resolved peaks, we observed peak interference causing distortions in mass and intensity, which is a well-described phenomenon in FTMS. Concentrations of respective species were more accurate when calculated from M+1. Moreover, some minor species, affected by considerable Type-II overlap, could only be quantified by M+1. Unexpectedly, even completely unresolved peaks were substantially overcorrected by Type-II correction because of peak interference. The described method was validated including intraday and interday precisions for human serum and fibroblast samples. Taken together, our results show that accurate quantification of lipid species by FTMS requires resolution-depended data analysis.
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Affiliation(s)
- Marcus Höring
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Regensburg, Germany
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sabrina Krautbauer
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Regensburg, Germany
| | - Verena M Ertl
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Regensburg, Germany
| | - Ralph Burkhardt
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Regensburg, Germany
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Regensburg, Germany.
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5
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Hofferek V, Su H, Reid GE. Chemical Derivatization-Aided High Resolution Mass Spectrometry for Shotgun Lipidome Analysis. Methods Mol Biol 2021; 2306:61-75. [PMID: 33954940 DOI: 10.1007/978-1-0716-1410-5_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Chemical derivatization coupled with nano-electrospray ionization (nESI) and ultra-high resolution accurate mass spectrometry (UHRAMS) is an established approach to overcome isobaric and isomeric mass interference limitations, and improve the analytical performance, of direct-infusion (i.e., "shotgun") lipidome analysis strategies for "sum composition" level identification and quantification of individual lipid species from within complex mixtures. Here, we describe a protocol for sequential functional group selective derivatization of aminophospholipids and O-alk-1'-enyl (i.e., plasmalogen) lipids, that when integrated into a shotgun lipidomics workflow involving deuterium-labeled internal lipid standard addition, monophasic lipid extraction, and nESI-UHRAMS analysis, enables the routine identification and quantification of >500 individual lipid species at the "sum composition" level, across four lipid categories and from >30 lipid classes and subclasses.
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Affiliation(s)
- Vinzenz Hofferek
- School of Chemistry, The University of Melbourne, Parkville, VIC, Australia
| | - Huaqi Su
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC, Australia.,The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Gavin E Reid
- School of Chemistry, The University of Melbourne, Parkville, VIC, Australia. .,Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC, Australia. .,Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia.
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6
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Djambazova KV, Klein DR, Migas LG, Neumann EK, Rivera ES, Van de Plas R, Caprioli RM, Spraggins JM. Resolving the Complexity of Spatial Lipidomics Using MALDI TIMS Imaging Mass Spectrometry. Anal Chem 2020; 92:13290-13297. [PMID: 32808523 DOI: 10.1021/acs.analchem.0c02520] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lipids are a structurally diverse class of molecules with important biological functions including cellular signaling and energy storage. Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) allows for direct mapping of biomolecules in tissues. Fully characterizing the structural diversity of lipids remains a challenge due to the presence of isobaric and isomeric species, which greatly complicates data interpretation when only m/z information is available. Integrating ion mobility separations aids in deconvoluting these complex mixtures and addressing the challenges of lipid IMS. Here, we demonstrate that a MALDI quadrupole time-of-flight (Q-TOF) mass spectrometer with trapped ion mobility spectrometry (TIMS) enables a >250% increase in the peak capacity during IMS experiments. MALDI TIMS-MS separation of lipid isomer standards, including sn backbone isomers, acyl chain isomers, and double-bond position and stereoisomers, is demonstrated. As a proof of concept, in situ separation and imaging of lipid isomers with distinct spatial distributions were performed using tissue sections from a whole-body mouse pup.
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Affiliation(s)
- Katerina V Djambazova
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States.,Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Dustin R Klein
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Lukasz G Migas
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Elizabeth K Neumann
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Emilio S Rivera
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Raf Van de Plas
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Richard M Caprioli
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States.,Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States.,Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, Tennessee 37232, United States.,Department of Medicine, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Jeffrey M Spraggins
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States.,Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
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7
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Höring M, Ekroos K, Baker PRS, Connell L, Stadler SC, Burkhardt R, Liebisch G. Correction of Isobaric Overlap Resulting from Sodiated Ions in Lipidomics. Anal Chem 2020; 92:10966-10970. [PMID: 32672443 DOI: 10.1021/acs.analchem.0c02408] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Lipidomic analyses aim for absolute quantification of lipid species profiles in biological samples. In past years, mass spectrometry (MS) methods based on high resolution accurate masses (HRAM) have increasingly been applied to identify and quantify lipid species on the MS level. This strategy requires consideration of isobaric overlaps which may also result from various adduct ions. Generally applied solvent additives favor the formation of protonated and ammoniated ions in positive ion mode, yet sodiated ions are also frequently observed. These sodiated ions interfere with protonated ions of the species of the same lipid class with two additional CH2 and three double bonds (Δm/z = 0.0025) and the first isotopic peak overlaps with ammoniated ions of a species with one additional CH2 and four double bonds (Δm/z = 0.0057). In this work, we present an algorithm based on the sodiated to protonated/ammoniated adduct ion ratios of applied internal standards to correct for these interferences. We could demonstrate that these ratios differ significantly between lipid classes but are affected by neither chain length nor number of double bonds within a lipid class. Finally, the algorithm is demonstrated for correcting human serum samples analyzed by Fourier-transform mass spectrometry (FTMS). Here, the application of sodium correction significantly reduced overestimations and misidentifications.
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Affiliation(s)
- Marcus Höring
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Irisviksvägen 31D, 02230 Esbo, Finland
| | - Paul R S Baker
- Avanti Polar Lipids, 700 Industrial Park Dr, Alabaster, Alabama 35007, United States
| | - Lisa Connell
- Avanti Polar Lipids, 700 Industrial Park Dr, Alabaster, Alabama 35007, United States
| | - Sonja C Stadler
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Ralph Burkhardt
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
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8
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Hu C, Duan Q, Han X. Strategies to Improve/Eliminate the Limitations in Shotgun Lipidomics. Proteomics 2020; 20:e1900070. [PMID: 31291508 PMCID: PMC7394605 DOI: 10.1002/pmic.201900070] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/15/2019] [Indexed: 11/05/2022]
Abstract
Direct infusion-based shotgun lipidomics is one of the most powerful and useful tools in comprehensive analysis of lipid species from lipid extracts of various biological samples with high accuracy/precision. However, despite many advantages, the classical shotgun lipidomics suffers some general dogmas of limitations, such as ion suppression, ambiguous identification of isobaric/isomeric lipid species, and ion source-generated artifacts, restraining the applications in analysis of low-abundance lipid species, particularly those less ionizable or isomers that yield almost identical fragmentation patterns. This article reviews the strategies (such as modifier addition, prefractionation, chemical derivatization, charge feature utilization) that have been employed to improve/eliminate these limitations in modern shotgun lipidomics approaches (e.g., high mass resolution mass spectrometry-based and multidimensional mass spectrometry-based shotgun lipidomics). Therefore, with the enhancement of these strategies for shotgun lipidomics, comprehensive analysis of lipid species including isomeric/isobaric species is achieved in a more accurate and effective manner, greatly substantiating the aberrant lipid metabolism, signaling trafficking, and homeostasis under pathological conditions.
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Affiliation(s)
- Changfeng Hu
- College of Basic Medical Sciences, Zhejiang Chinese Medical University, 548 Bingwen Road, Hangzhou, Zhejiang 310053, China
| | - Qiao Duan
- College of Basic Medical Sciences, Zhejiang Chinese Medical University, 548 Bingwen Road, Hangzhou, Zhejiang 310053, China
| | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229 USA
- Department of Medicine – Diabetes, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229 USA
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9
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Comprehensive lipidomics of mouse plasma using class-specific surrogate calibrants and SWATH acquisition for large-scale lipid quantification in untargeted analysis. Anal Chim Acta 2019; 1086:90-102. [PMID: 31561798 DOI: 10.1016/j.aca.2019.08.030] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 08/03/2019] [Accepted: 08/14/2019] [Indexed: 12/24/2022]
Abstract
Lipidomics has gained rising attention in recent years. Several strategies for lipidomic profiling have been developed, with targeted analysis of selected lipid species, typically utilized for lipid quantification by low-resolution triple quadrupole MS/MS, and untargeted analysis by high-resolution MS instruments, focusing on hypothesis generation for prognostic, diagnostic and/or disease-relevant biomarker discovery. The latter methodologies generally yield relative quantification data with limited inter-assay comparability. In this work we aimed to combine untargeted analysis and absolute quantification to enhance data quality and to obtain independent results for optimum comparability to previous studies or database entries. For the lipidomic analysis of mouse plasma, RP-UHPLC hyphenated to a high-resolution quadrupole TOF mass spectrometer in comprehensive data-independent SWATH acquisition mode was employed. This way, quantifiable data on the MS and the MS/MS level were recorded, which increases assay specificity and quantitative performance. Due to the lack of an appropriate blank matrix for untargeted lipidomics, we herein established a sophisticated strategy for lipid class-specific calibration with stable isotope labeled standards (surrogate calibrants). LLOQs were in the range between 10 and 50 ng mL-1 for LPC, LPE, PI, PS, PG, SM, PC, PE, DAG) or 100-700 ng mL-1 (MAG, TAG), except for cholesterol and CE (1-20 μg mL-1). Acceptable values for accuracy and precision well below ±15% bias were reached for the majority of surrogate calibrants. However, to achieve sufficient accuracy for target lipids, response factors to corresponding surrogate calibrants are required. An approach to estimate response factors via a standard reference material (NIST SRM 1950) was therefore conducted. Furthermore, a useful workflow for post-acquisition re-calibration, involving response factor determination and iteratively built libraries, is suggested. In comparison to single-point calibration, the presented surrogate calibrant method was shown to yield results with improved accuracy that are largely in accordance with standard addition. Quantitative results of real samples (high-fat diet vs control diet) were then compared to two previously published dietary mouse plasma studies that provided absolute lipid levels and showed similar trends.
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10
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Gathungu RM, Larrea P, Sniatynski MJ, Marur VR, Bowden JA, Koelmel JP, Starke-Reed P, Hubbard VS, Kristal BS. Optimization of Electrospray Ionization Source Parameters for Lipidomics To Reduce Misannotation of In-Source Fragments as Precursor Ions. Anal Chem 2018; 90:13523-13532. [PMID: 30265528 PMCID: PMC6297073 DOI: 10.1021/acs.analchem.8b03436] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Lipidomics requires the accurate annotation of lipids in complex samples to enable determination of their biological relevance. We demonstrate that unintentional in-source fragmentation (ISF, common in lipidomics) generates ions that have identical masses to other lipids. Lysophosphatidylcholines (LPC), for example, generate in-source fragments with the same mass as free fatty acids and lysophosphatidylethanolamines (LPE). The misannotation of in-source fragments as true lipids is particularly insidious in complex matrixes since most masses are initially unannotated and comprehensive lipid standards are unavailable. Indeed, we show such LPE/LPC misannotations are incorporated in the data submitted to the National Institute of Standards and Technology (NIST) interlaboratory comparison exercise. Computer simulations exhaustively identified potential misannotations. The selection of in-source fragments of highly abundant lipids as features, instead of the correct recognition of trace lipids, can potentially lead to (i) missing the biologically relevant lipids (i.e., a false negative) and/or (ii) incorrect assignation of a phenotype to an incorrect lipid (i.e., false positive). When ISF is not eliminated in the negative ion mode, ∼40% of the 100 most abundant masses corresponding to unique phospholipids measured in plasma were artifacts from ISF. We show that chromatographic separation and ion intensity considerations assist in distinguishing precursor ions from in-source fragments, suggesting ISF may be especially problematic when complex samples are analyzed via shotgun lipidomics. We also conduct a systematic evaluation of electrospray ionization (ESI) source parameters on an Exactive equipped with a heated electrospray ionization (HESI-II) source with the objective of obtaining uniformly appropriate source conditions for a wide range of lipids, while, at the same time, reducing in-source fragmentation.
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Affiliation(s)
- Rose M. Gathungu
- Department of Medicine, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital and Department of Medicine, Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115
| | - Pablo Larrea
- Department of Medicine, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital and Department of Medicine, Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115
| | - Matthew J. Sniatynski
- Department of Medicine, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital and Department of Medicine, Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115
| | - Vasant R. Marur
- Department of Medicine, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital and Department of Medicine, Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115
| | - John A. Bowden
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610
- National Institute of Standards and Technology, Hollings Marine Laboratory, Charleston, SC 29412
| | - Jeremy P. Koelmel
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610
| | - Pamela Starke-Reed
- Deputy Director, NIH Division of Nutrition Research Coordination, Bethesda, MD 20892
| | - Van S. Hubbard
- Director, NIH Division of Nutrition Research Coordination, Bethesda, MD 20892
| | - Bruce S. Kristal
- Department of Medicine, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital and Department of Medicine, Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115
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11
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Hsu FF. Mass spectrometry-based shotgun lipidomics - a critical review from the technical point of view. Anal Bioanal Chem 2018; 410:6387-6409. [PMID: 30094786 PMCID: PMC6195124 DOI: 10.1007/s00216-018-1252-y] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/03/2018] [Accepted: 07/06/2018] [Indexed: 11/24/2022]
Abstract
Over the past decade, mass spectrometry (MS)-based "shotgun lipidomics" has emerged as a powerful tool for quantitative and qualitative analysis of the complex lipids in the biological system. The aim of this critical review is to give the interested reader a concise overview of the current state of the technology, focused on lipidomic analysis by mass spectrometry. The pros and cons, and pitfalls associated with each available "shotgun lipidomics" method are discussed; and the new strategies for improving the current methods are described. A list of important papers and reviews that are sufficient rather than comprehensive, covering all the aspects of lipidomics including the workflow, methodology, and fundamentals is also compiled for readers to follow. Graphical abstract ᅟ.
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Affiliation(s)
- Fong-Fu Hsu
- Mass Spectrometry Resource, Division of Endocrinology, Diabetes, Metabolism, and Lipid Research, Department of Internal Medicine, Washington University School of Medicine, 660 S Euclid, St. Louis, MO, 63110, USA.
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12
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Schlotterbeck J, Chatterjee M, Gawaz M, Lämmerhofer M. Comprehensive MS/MS profiling by UHPLC-ESI-QTOF-MS/MS using SWATH data-independent acquisition for the study of platelet lipidomes in coronary artery disease. Anal Chim Acta 2018; 1046:1-15. [PMID: 30482286 DOI: 10.1016/j.aca.2018.08.060] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/29/2018] [Accepted: 08/30/2018] [Indexed: 01/13/2023]
Abstract
A non-targeted lipidomics workflow based on C8 core-shell particle ultra high-performance liquid chromatography (UHPLC) hyphenated to ESI-QTOF-MS in data-independent acquisition (DIA) mode with sequential window acquisition of all theoretical fragment ion spectra (SWATH) was developed and applied to differential platelet lipidomics profiling of cardiovascular disease patients (stable angina pectoris (n = 10), ST-elevated myocardial infarction (n = 13)) against healthy controls (n = 10). DIA with SWATH generates comprehensive MS and MS/MS data throughout the entire chromatograms and all study samples. Hence, chromatograms can be extracted based on precursors or fragments which provided some benefits in terms of assay specificity in some cases. SWATH acquisition offers flexible experimental design with variable Q1 isolation windows. Liquid chromatography as well as SWATH settings were optimized to cover the lipidome of human platelets. The flexibility of the SWATH experiment design was utilized to implement target SWATH windows with narrow 5 Da Q1 precursor ion selection width (multiple reaction monitoring (MRM)-like SWATH windows) for the detection of low abundant oxidized phospholipids. Data processing was performed with MS-DIAL, and its feasibilities and caveats are discussed by illustrative examples. Thereby, identification of lipids is still a bottleneck in non-targeted lipidomics workflow. MS-DIAL, however, offers automatic identification via spectral matching using an in silico library. In total 1971 molecular features were detected cross the samples of which 611 were identified (total score >70%). The quality of the acquired data was validated with embedded quality control samples (n = 11). 80.3% of all features detected in the QC samples showed a coefficient of variation of below 30%. Multivariate statistics were used to visualize differences in the lipidome of distinct sample groups at a false discovery rate of 5%.
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Affiliation(s)
- Jörg Schlotterbeck
- University of Tübingen, Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Madhumita Chatterjee
- Department of Cardiology and Cardiovascular Medicine, University Hospital Tübingen, Otfried-Müller-Strasse 10, 72076, Tübingen, Germany
| | - Meinrad Gawaz
- Department of Cardiology and Cardiovascular Medicine, University Hospital Tübingen, Otfried-Müller-Strasse 10, 72076, Tübingen, Germany
| | - Michael Lämmerhofer
- University of Tübingen, Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, Auf der Morgenstelle 8, 72076, Tübingen, Germany.
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13
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Wang M, Wang C, Han X. Selection of internal standards for accurate quantification of complex lipid species in biological extracts by electrospray ionization mass spectrometry-What, how and why? MASS SPECTROMETRY REVIEWS 2017; 36:693-714. [PMID: 26773411 PMCID: PMC4947032 DOI: 10.1002/mas.21492] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/28/2015] [Indexed: 05/20/2023]
Abstract
Lipidomics is rapidly expanding because of the great facilitation of recent advances in, and novel applications of, electrospray ionization mass spectrometry techniques. The greatest demands have been for successful quantification of lipid classes, subclasses, and individual molecular species in biological samples at acceptable accuracy. This review addresses the selection of internal standards in different methods for accurate quantification of individual lipid species. The principles of quantification with electrospray ionization mass spectrometry are first discussed to recognize the essentials for quantification. The basics of different lipidomics approaches are overviewed to understand the variables that need to be considered for accurate quantification. The factors that affect accurate quantification are extensively discussed, and the solutions to resolve these factors are proposed-largely through addition of internal standards. Finally, selection of internal standards for different methods is discussed in detail to address the issues of what, how, and why related to internal standards. We believe that thorough discussion of the topics related to internal standards should aid in quantitative analysis of lipid classes, subclasses, and individual molecular species and should have big impacts on advances in lipidomics. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:693-714, 2017.
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Affiliation(s)
- Miao Wang
- Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL 32827 USA
| | - Chunyan Wang
- Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL 32827 USA
| | - Xianlin Han
- Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL 32827 USA
- College of Basic Medical Sciences, Zhejiang Chinese Medical University, 548 Bingwen Road, Hangzhou, Zhejiang 310053, China
- To whom correspondence should be addressed: Xianlin Han, Ph.D., Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute, 6400 Sanger Road, Orlando, Florida 32827, USA, Telephone: (407) 745-2139, Fax: (407) 745-2016,
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14
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Satomi Y, Hirayama M, Kobayashi H. One-step lipid extraction for plasma lipidomics analysis by liquid chromatography mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1063:93-100. [PMID: 28850891 DOI: 10.1016/j.jchromb.2017.08.020] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 08/01/2017] [Accepted: 08/15/2017] [Indexed: 12/20/2022]
Abstract
In the past decade, various lipidomics methodologies have been developed using mass spectrometry based analytical technologies, enabling wide coverage lipid detection in a quantitative manner. Hence, lipidomics has become a widely-accepted approach for biomarker discovery and mechanism elucidation in both medical and biology research fields; however, there are still technical challenges. In this study, focusing on the sample preparation procedure, a single step deproteinization by a water-soluble organic solvent, such as methanol (MeOH), ethanol (EtOH), isopropanol (IPA) or acetonitrile (ACN), was evaluated and proved to be satisfactory for lipidomics analysis. Moreover, during this investigation ACN deproteinization was revealed to not be an effective method for lipid extraction because lipid decomposition was observed during the protein precipitation process through lipase activation, potentially due to the insufficient protein denaturation. Therefore, excluding ACN, protein precipitation by alcohol was evaluated as the lipid extraction reagent. Moreover, adding the MTBE-MeOH (mMM) method, one of the major liquid-liquid extraction methods for shotgun lipidomics, these four approaches were compared. Lipids were extracted from mouse plasma by these four methods and used for exhaustive lipid profiling by liquid chromatography mass spectrometry (LC/MS) analysis. Comparison of these four methods revealed that alcohol based protein precipitation was a useful sample preparation procedure for LC/MS based lipidomics analysis. Whereas MeOH extraction was appropriate for hydrophilic lipid species, IPA was effective for hydrophobic lipids such as triacylglycerols (TG). In practice, EtOH extraction is thought to be the best approach to cover wide range of lipid species using a simple preparation procedure.
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Affiliation(s)
- Yoshinori Satomi
- Integrated Technology Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Japan.
| | - Megumi Hirayama
- Integrated Technology Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Japan
| | - Hiroyuki Kobayashi
- Integrated Technology Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Japan.
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15
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Wang M, Palavicini JP, Cseresznye A, Han X. Strategy for Quantitative Analysis of Isomeric Bis(monoacylglycero)phosphate and Phosphatidylglycerol Species by Shotgun Lipidomics after One-Step Methylation. Anal Chem 2017; 89:8490-8495. [PMID: 28708380 DOI: 10.1021/acs.analchem.7b02058] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Understanding the cellular function and metabolism of bis(monoacylglycero)phosphate (BMP), an important but low-abundance class of phospholipids, has been hindered due to its difficulties to be resolved from its structural isomer (i.e., phosphatidylglycerol, PG, another low-abundance class of phospholipids). A novel strategy for quantitative analysis of BMP and PG species was developed after one-step methylation of lipid extracts in combination with high mass accuracy/resolution mass spectrometry after direct infusion (i.e., shotgun lipidomics). The novel strategy was applied for quantitative analysis of mouse hepatic BMP and PG species and their changes induced by long-term high-fat diet (HFD) feeding. Interestingly, we revealed that HFD-fed mice display a dramatic accumulation of hepatic BMP compared to chow-fed littermates. We believe the development of this novel strategy could greatly facilitate our understanding of the role of BMP in biological systems.
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Affiliation(s)
- Miao Wang
- Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute , Orlando, Florida 32827, United States
| | - Juan Pablo Palavicini
- Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute , Orlando, Florida 32827, United States
| | - Adam Cseresznye
- Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute , Orlando, Florida 32827, United States
| | - Xianlin Han
- Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute , Orlando, Florida 32827, United States
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16
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Rampler E, Coman C, Hermann G, Sickmann A, Ahrends R, Koellensperger G. LILY-lipidome isotope labeling of yeast: in vivo synthesis of 13C labeled reference lipids for quantification by mass spectrometry. Analyst 2017; 142:1891-1899. [PMID: 28475182 DOI: 10.1039/c7an00107j] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Quantification is an essential task in comprehensive lipidomics studies challenged by the high number of lipids, their chemical diversity and their dynamic range of the lipidome. In this work, we introduce lipidome isotope labeling of yeast (LILY) in order to produce (non-radioactive) isotopically labeled eukaryotic lipid standards in yeast for normalization and quantification in mass spectrometric assays. More specifically, LILY is a fast and efficient in vivo labeling strategy in Pichia pastoris for the production of 13C labeled lipid library further paving the way to comprehensive compound-specific internal standardization in quantitative mass spectrometry based assays. More than 200 lipid species (from PA, PC, PE, PG, PI, PS, LysoGP, CL, DAG, TAG, DMPE, Cer, HexCer, IPC, MIPC) were obtained from yeast extracts with an excellent 13C enrichment >99.5%, as determined by complementary high resolution mass spectrometry based shotgun and high resolution LC-MS/MS analysis. In a first proof of principle study we tested the relative and absolute quantification capabilities of the 13C enriched lipids obtained by LILY using a parallel reaction monitoring based LC-MS approach. In relative quantification it could be shown that compound specific internal standardization was essential for the accuracy extending the linear dynamic range to four orders of magnitude. Excellent analytical figures of merit were observed for absolute quantification for a selected panel of 5 investigated glycerophospholipids (e.g. LOQs around 5 fmol absolute; typical concentrations ranging between 1 to 10 nmol per 108 yeast cell starting material; RSDs <10% (N = 4)).
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Affiliation(s)
- Evelyn Rampler
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 38, 1090 Vienna, Austria. and Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria and Chemistry Meets Microbiolgy, Althanstraße 14, 1090 Vienna, Austria
| | - Cristina Coman
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Gerrit Hermann
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 38, 1090 Vienna, Austria. and ISOtopic Solutions, Währingerstr. 38, 1090 Vienna, Austria
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany and College of Physical Sciences, University of Aberdeen, Department of Chemistry, AB24 3UE Aberdeen, UK and Medizinische Fakultät, Medizinische Proteom-Center (MCP), Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Robert Ahrends
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Gunda Koellensperger
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 38, 1090 Vienna, Austria. and Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria and Chemistry Meets Microbiolgy, Althanstraße 14, 1090 Vienna, Austria
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17
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Han X. Lipidomics for precision medicine and metabolism: A personal view. Biochim Biophys Acta Mol Cell Biol Lipids 2017; 1862:804-807. [PMID: 28238864 DOI: 10.1016/j.bbalip.2017.02.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 02/18/2017] [Accepted: 02/21/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Xianlin Han
- Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute, 6400 Sanger Road, Orlando, FL 32827, USA.
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18
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Bielow C, Mastrobuoni G, Orioli M, Kempa S. On Mass Ambiguities in High-Resolution Shotgun Lipidomics. Anal Chem 2017; 89:2986-2994. [PMID: 28193003 DOI: 10.1021/acs.analchem.6b04456] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Mass-spectrometry-based lipidomics aims to identify as many lipid species as possible from complex biological samples. Due to the large combinatorial search space, unambiguous identification of lipid species is far from trivial. Mass ambiguities are common in direct-injection shotgun experiments, where an orthogonal separation (e.g., liquid chromatography) is missing. Using the rich information within available lipid databases, we generated a comprehensive rule set describing mass ambiguities, while taking into consideration the resolving power (and its decay) of different mass analyzers. Importantly, common adduct species and isotopic peaks are accounted for and are shown to play a major role, both for perfect mass overlaps due to identical sum formulas and resolvable mass overlaps. We identified known and hitherto unknown mass ambiguities in high- and ultrahigh resolution data, while also ranking lipid classes by their propensity to cause ambiguities. On the basis of this new set of ambiguity rules, guidelines and recommendations for experimentalists and software developers of what constitutes a solid lipid identification in both MS and MS/MS were suggested. For researchers new to the field, our results are a compact source of ambiguities which should be accounted for. These new findings also have implications for the selection of internal standards, peaks used for internal mass calibration, optimal choice of instrument resolution, and sample preparation, for example, in regard to adduct ion formation.
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Affiliation(s)
- Chris Bielow
- Berlin Institute of Health Technology Platform Metabolomics, Max-Delbrück-Centrum for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Guido Mastrobuoni
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Marica Orioli
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Stefan Kempa
- Berlin Institute of Health Technology Platform Metabolomics, Max-Delbrück-Centrum for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany.,Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
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19
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Ryan E, Reid GE. Chemical Derivatization and Ultrahigh Resolution and Accurate Mass Spectrometry Strategies for "Shotgun" Lipidome Analysis. Acc Chem Res 2016; 49:1596-604. [PMID: 27575732 DOI: 10.1021/acs.accounts.6b00030] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Lipids play critical structural and functional roles in the regulation of cellular homeostasis, and it is increasingly recognized that the disruption of lipid metabolism or signaling or both is associated with the onset and progression of certain metabolically linked diseases. As a result, the field of lipidomics has emerged to comprehensively identify and structurally characterize the diverse range of lipid species within a sample of interest and to quantitatively monitor their abundances under different physiological or pathological conditions. Mass spectrometry (MS) has become a critical enabling platform technology for lipidomic researchers. However, the presence of isobaric (i.e., same nominal mass) and isomeric (i.e., same exact mass) lipids within complex lipid extracts means that MS-based identification and quantification of individual lipid species remains a significant analytical challenge. Ultrahigh resolution and accurate mass spectrometry (UHRAMS) offers a convenient solution to the isobaric mass overlap problem, while a range of chromatographic separation, differential extraction, intrasource separation and selective ionization methods, or tandem mass spectrometry (MS/MS) strategies may be used to address some types of isomeric mass lipid overlaps. Alternatively, chemical derivatization strategies represent a more recent approach for the separation of lipids within complex mixtures, including for isomeric lipids. In this Account, we highlight the key components of a lipidomics workflow developed in our laboratory, whereby certain lipid classes or subclasses, namely, aminophospholipids and O-alk-1'-enyl (i.e., plasmalogen) ether-containing lipids, are shifted in mass following sequential functional group selective chemical derivatization reactions prior to "shotgun" nano-ESI-UHRAMS analysis, "targeted" MS/MS, and automated database searching. This combined derivatization and UHRAMS approach resolves both isobaric mass lipids and certain categories of isomeric mass lipids within crude lipid extracts, with no requirement for extensive sample handling prior to analysis, with additional potential for enhanced ionization efficiencies, improved molecular level structural characterization, and multiplexed relative quantification. When integrated with a monophasic method for the simultaneous global extraction of both highly polar and nonpolar lipids, this workflow has been shown to enable the sum composition level identification and relative quantification of 500-600 individual lipid species across four lipid categories and from 36 lipid classes and subclasses, in only 1-2 min data acquisition time and with minimal sample consumption. Thus, while some analytical challenges remain to be addressed, shotgun lipidomics workflows encompassing chemical derivatization strategies have particular promise for the analysis of samples with limited availability that require rapid and unbiased assessment of global lipid metabolism.
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Affiliation(s)
- Eileen Ryan
- School
of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Gavin E. Reid
- School
of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia
- Department
of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
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20
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Yang K, Han X. Lipidomics: Techniques, Applications, and Outcomes Related to Biomedical Sciences. Trends Biochem Sci 2016; 41:954-969. [PMID: 27663237 DOI: 10.1016/j.tibs.2016.08.010] [Citation(s) in RCA: 341] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/16/2016] [Accepted: 08/19/2016] [Indexed: 12/16/2022]
Abstract
Lipidomics is a newly emerged discipline that studies cellular lipids on a large scale based on analytical chemistry principles and technological tools, particularly mass spectrometry. Recently, techniques have greatly advanced and novel applications of lipidomics in the biomedical sciences have emerged. This review provides a timely update on these aspects. After briefly introducing the lipidomics discipline, we compare mass spectrometry-based techniques for analysis of lipids and summarize very recent applications of lipidomics in health and disease. Finally, we discuss the status of the field, future directions, and advantages and limitations of the field.
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Affiliation(s)
- Kui Yang
- Division of Bioorganic Chemistry and Molecular Pharmacology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xianlin Han
- Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida 32827, USA; College of Basic Medical Sciences, Zhejiang Chinese Medical University, 548 Bingwen Road, Hangzhou, Zhejiang 310053, China.
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21
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Ghaste M, Mistrik R, Shulaev V. Applications of Fourier Transform Ion Cyclotron Resonance (FT-ICR) and Orbitrap Based High Resolution Mass Spectrometry in Metabolomics and Lipidomics. Int J Mol Sci 2016; 17:ijms17060816. [PMID: 27231903 PMCID: PMC4926350 DOI: 10.3390/ijms17060816] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/14/2016] [Accepted: 05/17/2016] [Indexed: 02/02/2023] Open
Abstract
Metabolomics, along with other "omics" approaches, is rapidly becoming one of the major approaches aimed at understanding the organization and dynamics of metabolic networks. Mass spectrometry is often a technique of choice for metabolomics studies due to its high sensitivity, reproducibility and wide dynamic range. High resolution mass spectrometry (HRMS) is a widely practiced technique in analytical and bioanalytical sciences. It offers exceptionally high resolution and the highest degree of structural confirmation. Many metabolomics studies have been conducted using HRMS over the past decade. In this review, we will explore the latest developments in Fourier transform mass spectrometry (FTMS) and Orbitrap based metabolomics technology, its advantages and drawbacks for using in metabolomics and lipidomics studies, and development of novel approaches for processing HRMS data.
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Affiliation(s)
- Manoj Ghaste
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, Denton, TX 76203, USA.
| | | | - Vladimir Shulaev
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, Denton, TX 76203, USA.
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22
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Optimizing the lipidomics workflow for clinical studies—practical considerations. Anal Bioanal Chem 2015; 407:4973-93. [DOI: 10.1007/s00216-015-8633-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 03/08/2015] [Accepted: 03/11/2015] [Indexed: 12/19/2022]
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23
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Wang C, Wang M, Han X. Applications of mass spectrometry for cellular lipid analysis. MOLECULAR BIOSYSTEMS 2015; 11:698-713. [PMID: 25598407 PMCID: PMC4376555 DOI: 10.1039/c4mb00586d] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Mass spectrometric analysis of cellular lipids is an enabling technology for lipidomics, which is a rapidly-developing research field. In this review, we briefly discuss the principles, advantages, and possible limitations of electrospray ionization (ESI) and matrix assisted laser desorption/ionization (MALDI) mass spectrometry-based methodologies for the analysis of lipid species. The applications of these methodologies to lipidomic research are also summarized.
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Affiliation(s)
- Chunyan Wang
- Diabetes and Obesity Research Center, Sanford-Burnham Medical Research Institute, 6400 Sanger Road, Orlando, Florida 32827, USA.
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