1
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Scoggins TR, Specker JT, Prentice BM. Multiple ion isolation and accumulation events for selective chemical noise reduction and dynamic range enhancement in MALDI imaging mass spectrometry. Analyst 2024; 149:2459-2468. [PMID: 38525787 PMCID: PMC11149414 DOI: 10.1039/d4an00160e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Abundant chemical noise in MALDI imaging mass spectrometry experiments can impede the detection of less abundant compounds of interest. This chemical noise commonly originates from the MALDI matrix as well as other endogenous compounds present in high concentrations and/or with high ionization efficiencies. MALDI imaging mass spectrometry of biological tissues measures numerous biomolecular compounds that exist in a wide range of concentrations in vivo. When ion trapping instruments are used, highly abundant ions can dominate the charge capacity and lead to space charge effects that hinder the dynamic range and detection of lowly abundant compounds of interest. Gas-phase fractionation has been previously utilized in mass spectrometry to isolate and enrich target analytes. Herein, we have characterized the use of multiple continuous accumulations of selected ions (Multi CASI) to reduce the abundance of chemical noise and diminish the effects of space charge in MALDI imaging mass spectrometry experiments. Multi CASI utilizes the mass-resolving capability of a quadrupole mass filter to perform multiple sequential ion isolation events prior to a single mass analysis of the combined ion population. Multi CASI was used to improve metabolite and lipid detection in the MALDI imaging mass spectrometry analysis of rat brain tissue.
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Affiliation(s)
- Troy R Scoggins
- Department of Chemistry, University of Florida, Gainesville, FL, USA.
| | | | - Boone M Prentice
- Department of Chemistry, University of Florida, Gainesville, FL, USA.
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2
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Kedia K, Harris R, Ekroos K, Moser KW, DeBord D, Tiberi P, Goracci L, Zhang NR, Wang W, Spellman DS, Bateman K. Investigating Performance of the SLIM-Based High Resolution Ion Mobility Platform for Separation of Isomeric Phosphatidylcholine Species. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2176-2186. [PMID: 37703523 DOI: 10.1021/jasms.3c00157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Lipids are structurally diverse molecules that play a pivotal role in a plethora of biological processes. However, deciphering the biological roles of the specific lipids is challenging due to the existence of numerous isomers. This high chemical complexity of the lipidome is one of the major challenges in lipidomics research, as the traditional liquid chromatography-mass spectrometry (LC-MS) based approaches are often not powerful enough to resolve these isomeric and isobaric nuances within complex samples. Thus, lipids are uniquely suited to the benefits provided by multidimensional liquid chromatography-ion mobility-mass spectrometry (LC-IM-MS) analysis. However, many forms of lipid isomerism, including double-bond positional isomers and regioisomers, are structurally similar such that their collision cross section (CCS) differences are unresolvable via conventional IM approaches. Here we evaluate the performance of a high resolution ion mobility (HRIM) system based on structures for lossless ion manipulation (SLIM) technology interfaced to a high resolution quadrupole time-of-flight (QTOF) analyzer to address the noted lipidomic isomerism challenge. SLIM implements the traveling wave ion mobility technique along an ∼13 m ion path, providing longer path lengths to enable improved separation of isomeric features. We demonstrate the power of HRIM-MS to dissect isomeric PC standards differing only in double bond (DB) and stereospecific number (SN) positions. The partial separation of protonated DB isomers is significantly enhanced when they are analyzed as metal adducts. For sodium adducts, we achieve close to baseline separation of three different PC 18:1/18:1 isomers with different cis-double bond locations. Similarly, PC 18:1/18:1 (cis-9) can be resolved from the corresponding PC 18:1/18:1 (trans-9) form. The separation capacity is further enhanced when using silver ion doping, enabling the baseline separation of regioisomers that cannot be resolved when measured as sodium adducts. The sensitivity and reproducibility of the approach were assessed, and the performance for more complex mixtures was benchmarked by identifying PC isomers in total brain and liver lipid extracts.
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Affiliation(s)
- Komal Kedia
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Rachel Harris
- MOBILion Systems, Inc., Chadds Ford, Pennsylvania 19317, United States
| | - Kim Ekroos
- Lipidomics Consulting Ltd, Irisviksvägen 31D, 02230 Esbo, Finland
| | - Kelly W Moser
- MOBILion Systems, Inc., Chadds Ford, Pennsylvania 19317, United States
| | - Daniel DeBord
- MOBILion Systems, Inc., Chadds Ford, Pennsylvania 19317, United States
| | - Paolo Tiberi
- Molecular Discovery Ltd., Centennial Park, Borehamwood, Hertfordshire WD6 3FG United Kingdom
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | | | - Weixun Wang
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | | | - Kevin Bateman
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
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3
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Wang D, Xiao H, Lv X, Chen H, Wei F. Mass Spectrometry Based on Chemical Derivatization Has Brought Novel Discoveries to Lipidomics: A Comprehensive Review. Crit Rev Anal Chem 2023:1-32. [PMID: 37782560 DOI: 10.1080/10408347.2023.2261130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Lipids, as one of the most important organic compounds in organisms, are important components of cells and participate in energy storage and signal transduction of living organisms. As a rapidly rising field, lipidomics research involves the identification and quantification of multiple classes of lipid molecules, as well as the structure, function, dynamics, and interactions of lipids in living organisms. Due to its inherent high selectivity and high sensitivity, mass spectrometry (MS) is the "gold standard" analysis technique for small molecules in biological samples. The combination chemical derivatization with MS detection is a unique strategy that could improve MS ionization efficiency, facilitate structure identification and quantitative analysis. Herein, this review discusses derivatization-based MS strategies for lipidomic analysis over the past decade and focuses on all the reported lipid categories, including fatty acids and modified fatty acids, glycerolipids, glycerophospholipids, sterols and saccharolipids. The functional groups of lipids mainly involved in chemical derivatization include the C=C group, carboxyl group, hydroxyl group, amino group, carbonyl group. Furthermore, representative applications of these derivatization-based lipid profiling methods were summarized. Finally, challenges and countermeasures of lipid derivatization are mentioned and highlighted to guide future studies of derivatization-based MS strategy in lipidomics.
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Affiliation(s)
- Dan Wang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Oilseeds Processing of Ministry of Agriculture, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan, Hubei, PR China
| | - Huaming Xiao
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Oilseeds Processing of Ministry of Agriculture, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan, Hubei, PR China
| | - Xin Lv
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Oilseeds Processing of Ministry of Agriculture, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan, Hubei, PR China
| | - Hong Chen
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Oilseeds Processing of Ministry of Agriculture, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan, Hubei, PR China
| | - Fang Wei
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Oilseeds Processing of Ministry of Agriculture, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan, Hubei, PR China
- Hubei Hongshan Laboratory, Wuhan, Hubei, PR China
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4
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Zhang R, Ashford NK, Li A, Ross DH, Werth BJ, Xu L. High-throughput analysis of lipidomic phenotypes of methicillin-resistant Staphylococcus aureus by coupling in situ 96-well cultivation and HILIC-ion mobility-mass spectrometry. Anal Bioanal Chem 2023; 415:6191-6199. [PMID: 37535099 PMCID: PMC11059195 DOI: 10.1007/s00216-023-04890-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 08/04/2023]
Abstract
Antimicrobial resistance is a major threat to human health as resistant pathogens spread globally, and the development of new antimicrobials is slow. Since many antimicrobials function by targeting cell wall and membrane components, high-throughput lipidomics for bacterial phenotyping is of high interest for researchers to unveil lipid-mediated pathways when dealing with a large number of lab-selected or clinical strains. However, current practice for lipidomic analysis requires the cultivation of bacteria on a large scale, which does not replicate the growth conditions for high-throughput bioassays that are normally carried out in 96-well plates, such as susceptibility tests, growth curve measurements, and biofilm quantitation. Analysis of bacteria grown under the same condition as other bioassays would better inform the differences in susceptibility and other biological metrics. In this work, a high-throughput method for cultivation and lipidomic analysis of antimicrobial-resistant bacteria was developed for standard 96-well plates exemplified by methicillin-resistant Staphylococcus aureus (MRSA). By combining a 30-mm liquid chromatography (LC) column with ion mobility (IM) separation, elution time could be dramatically shortened to 3.6 min for a single LC run without losing major lipid features. Peak capacity was largely rescued by the addition of the IM dimension. Through multi-linear calibration, the deviation of retention time can be limited to within 5%, making database-based automatic lipid identification feasible. This high-throughput method was further validated by characterizing the lipidomic phenotypes of antimicrobial-resistant mutants derived from the MRSA strain, W308, grown in a 96-well plate.
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Affiliation(s)
- Rutan Zhang
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Nate K Ashford
- Department of Pharmacy, University of Washington, Seattle, WA, 98195, USA
| | - Amy Li
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Dylan H Ross
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, 98195, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, WA, 99352, Richland, USA
| | - Brian J Werth
- Department of Pharmacy, University of Washington, Seattle, WA, 98195, USA
| | - Libin Xu
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, 98195, USA.
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5
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Specker JT, Prentice BM. Separation of Isobaric Lipids in Imaging Mass Spectrometry Using Gas-Phase Charge Inversion Ion/Ion Reactions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1868-1878. [PMID: 37276072 PMCID: PMC10641901 DOI: 10.1021/jasms.3c00081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The diverse array of chemical compounds present in tissue samples results in many isobaric (i.e., same nominal mass) compounds in imaging mass spectrometry experiments. Adequate separation and differentiation of these compounds is necessary to ensure accurate analyte identification and avoid composite images comprising multiple compounds. High-resolution accurate mass (HRAM) measurements are able to resolve these compounds in some instances, but HRAM measurements are not always feasible depending on the instrument platform and the desired experimental time scale. Alternatively, tandem mass spectrometry (MS/MS) can be used to perform gas-phase transformations that improve molecular specificity. While conventional MS/MS methods employ collision induced dissociation (CID) to fragment compounds of interest and then analyze the product masses, gas-phase ion/ion reactions can be used to instead selectively react with desired classes of analytes. Herein, we have used gas-phase charge inversion ion/ion reactions to selectively resolve phosphatidylcholines (PCs) in isobaric lipid mixtures. A 1,4-phenylenedipropionic acid (PDPA) reagent dianion readily reacts with [M + H]+, [M + Na]+, and [M + K]+ ion types to produce demethylated product anions for each PC, [PC - CH3]-. These product anions are no longer isobaric and now differ in mass by 22 Da (protonated versus sodiated) and 16 Da (sodiated versus potassiated), respectively. This reaction has been used to differentiate isobaric lipids in the imaging mass spectrometry analysis of rat brain tissue.
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Affiliation(s)
| | - Boone M. Prentice
- Department of Chemistry, University of Florida, Gainesville, FL 32611
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6
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Nagy K, Gellén G, Papp D, Schlosser G, Révész Á. Optimum collision energies for proteomics: The impact of ion mobility separation. JOURNAL OF MASS SPECTROMETRY : JMS 2023; 58:e4957. [PMID: 37415399 DOI: 10.1002/jms.4957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/28/2023] [Accepted: 06/19/2023] [Indexed: 07/08/2023]
Abstract
Ion mobility spectrometry (IMS) is a widespread separation technique used in various research fields. It can be coupled to liquid chromatography-mass spectrometry (LC-MS/MS) methods providing an additional separation dimension. During IMS, ions are subjected to multiple collisions with buffer gas, which may cause significant ion heating. The present project addresses this phenomenon from the bottom-up proteomics point of view. We performed LC-MS/MS measurements on a cyclic ion mobility mass spectrometer with varied collision energy (CE) settings both with and without IMS. We investigated the CE dependence of identification score, using Byonic search engine, for more than 1000 tryptic peptides from HeLa digest standard. We determined the optimal CE values-giving the highest identification score-for both setups (i.e., with and without IMS). Results show that lower CE is advantageous when IMS separation is applied, by 6.3 V on average. This value belongs to the one-cycle separation configuration, and multiple cycles may supposedly have even larger impact. The effect of IMS is also reflected in the trends of optimal CE values versus m/z functions. The parameters suggested by the manufacturer were found to be almost optimal for the setup without IMS; on the other hand, they are obviously too high with IMS. Practical consideration on setting up a mass spectrometric platform hyphenated to IMS is also presented. Furthermore, the two CID (collision induced dissociation) fragmentation cells of the instrument-located before and after the IMS cell-were also compared, and we found that CE adjustment is needed when the trap cell is used for activation instead of the transfer cell. Data have been deposited in the MassIVE repository (MSV000090944).
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Affiliation(s)
- Kinga Nagy
- MS Proteomics Research Group, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
- Hevesy György PhD School of Chemistry, Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Gabriella Gellén
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Dávid Papp
- Hevesy György PhD School of Chemistry, Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Gitta Schlosser
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Ágnes Révész
- MS Proteomics Research Group, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
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7
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Kartowikromo KY, Olajide OE, Hamid AM. Collision cross section measurement and prediction methods in omics. JOURNAL OF MASS SPECTROMETRY : JMS 2023; 58:e4973. [PMID: 37620034 PMCID: PMC10530098 DOI: 10.1002/jms.4973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/26/2023] [Accepted: 07/20/2023] [Indexed: 08/26/2023]
Abstract
Omics studies such as metabolomics, lipidomics, and proteomics have become important for understanding the mechanisms in living organisms. However, the compounds detected are structurally different and contain isomers, with each structure or isomer leading to a different result in terms of the role they play in the cell or tissue in the organism. Therefore, it is important to detect, characterize, and elucidate the structures of these compounds. Liquid chromatography and mass spectrometry have been utilized for decades in the structure elucidation of key compounds. While prediction models of parameters (such as retention time and fragmentation pattern) have also been developed for these separation techniques, they have some limitations. Moreover, ion mobility has become one of the most promising techniques to give a fingerprint to these compounds by determining their collision cross section (CCS) values, which reflect their shape and size. Obtaining accurate CCS enables its use as a filter for potential analyte structures. These CCS values can be measured experimentally using calibrant-independent and calibrant-dependent approaches. Identification of compounds based on experimental CCS values in untargeted analysis typically requires CCS references from standards, which are currently limited and, if available, would require a large amount of time for experimental measurements. Therefore, researchers use theoretical tools to predict CCS values for untargeted and targeted analysis. In this review, an overview of the different methods for the experimental and theoretical estimation of CCS values is given where theoretical prediction tools include computational and machine modeling type approaches. Moreover, the limitations of the current experimental and theoretical approaches and their potential mitigation methods were discussed.
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Affiliation(s)
| | - Orobola E Olajide
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama, USA
| | - Ahmed M Hamid
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama, USA
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8
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Ross DH, Guo J, Bilbao A, Huan T, Smith RD, Zheng X. Evaluating Software Tools for Lipid Identification from Ion Mobility Spectrometry-Mass Spectrometry Lipidomics Data. Molecules 2023; 28:molecules28083483. [PMID: 37110719 PMCID: PMC10142755 DOI: 10.3390/molecules28083483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/12/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The unambiguous identification of lipids is a critical component of lipidomics studies and greatly impacts the interpretation and significance of analyses as well as the ultimate biological understandings derived from measurements. The level of structural detail that is available for lipid identifications is largely determined by the analytical platform being used. Mass spectrometry (MS) coupled with liquid chromatography (LC) is the predominant combination of analytical techniques used for lipidomics studies, and these methods can provide fairly detailed lipid identification. More recently, ion mobility spectrometry (IMS) has begun to see greater adoption in lipidomics studies thanks to the additional dimension of separation that it provides and the added structural information that can support lipid identification. At present, relatively few software tools are available for IMS-MS lipidomics data analysis, which reflects the still limited adoption of IMS as well as the limited software support. This fact is even more pronounced for isomer identifications, such as the determination of double bond positions or integration with MS-based imaging. In this review, we survey the landscape of software tools that are available for the analysis of IMS-MS-based lipidomics data and we evaluate lipid identifications produced by these tools using open-access data sourced from the peer-reviewed lipidomics literature.
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Affiliation(s)
- Dylan H Ross
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Jian Guo
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver Campus, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Aivett Bilbao
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Tao Huan
- Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver Campus, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Richard D Smith
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Xueyun Zheng
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA
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Camunas-Alberca SM, Moran-Garrido M, Sáiz J, Gil-de-la-Fuente A, Barbas C, Gradillas A. Integrating the potential of ion mobility spectrometry-mass spectrometry in the separation and structural characterisation of lipid isomers. Front Mol Biosci 2023; 10:1112521. [PMID: 37006618 PMCID: PMC10060977 DOI: 10.3389/fmolb.2023.1112521] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/14/2023] [Indexed: 03/18/2023] Open
Abstract
It is increasingly evident that a more detailed molecular structure analysis of isomeric lipids is critical to better understand their roles in biological processes. The occurrence of isomeric interference complicates conventional tandem mass spectrometry (MS/MS)-based determination, necessitating the development of more specialised methodologies to separate lipid isomers. The present review examines and discusses recent lipidomic studies based on ion mobility spectrometry combined with mass spectrometry (IMS-MS). Selected examples of the separation and elucidation of structural and stereoisomers of lipids are described based on their ion mobility behaviour. These include fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, and sterol lipids. Recent approaches for specific applications to improve isomeric lipid structural information using direct infusion, coupling imaging, or liquid chromatographic separation workflows prior to IMS-MS are also discussed, including: 1) strategies to improve ion mobility shifts; 2) advanced tandem MS methods based on activation of lipid ions with electrons or photons, or gas-phase ion-molecule reactions; and 3) the use of chemical derivatisation techniques for lipid characterisation.
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Affiliation(s)
- Sandra M. Camunas-Alberca
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
| | - Maria Moran-Garrido
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
| | - Jorge Sáiz
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
| | - Alberto Gil-de-la-Fuente
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
- Departamento de Tecnologías de la Información, Escuela Politécnica Superior, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
| | - Ana Gradillas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, Spain
- *Correspondence: Ana Gradillas,
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Zandl-Lang M, Plecko B, Köfeler H. Lipidomics-Paving the Road towards Better Insight and Precision Medicine in Rare Metabolic Diseases. Int J Mol Sci 2023; 24:ijms24021709. [PMID: 36675224 PMCID: PMC9866746 DOI: 10.3390/ijms24021709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Even though the application of Next-Generation Sequencing (NGS) has significantly facilitated the identification of disease-associated mutations, the diagnostic rate of rare diseases is still below 50%. This causes a diagnostic odyssey and prevents specific treatment, as well as genetic counseling for further family planning. Increasing the diagnostic rate and reducing the time to diagnosis in children with unclear disease are crucial for a better patient outcome and improvement of quality of life. In many cases, NGS reveals variants of unknown significance (VUS) that need further investigations. The delineation of novel (lipid) biomarkers is not only crucial to prove the pathogenicity of VUS, but provides surrogate parameters for the monitoring of disease progression and therapeutic interventions. Lipids are essential organic compounds in living organisms, serving as building blocks for cellular membranes, energy storage and signaling molecules. Among other disorders, an imbalance in lipid homeostasis can lead to chronic inflammation, vascular dysfunction and neurodegenerative diseases. Therefore, analyzing lipids in biological samples provides great insight into the underlying functional role of lipids in healthy and disease statuses. The method of choice for lipid analysis and/or huge assemblies of lipids (=lipidome) is mass spectrometry due to its high sensitivity and specificity. Due to the inherent chemical complexity of the lipidome and the consequent challenges associated with analyzing it, progress in the field of lipidomics has lagged behind other omics disciplines. However, compared to the previous decade, the output of publications on lipidomics has increased more than 17-fold within the last decade and has, therefore, become one of the fastest-growing research fields. Combining multiple omics approaches will provide a unique and efficient tool for determining pathogenicity of VUS at the functional level, and thereby identifying rare, as well as novel, genetic disorders by molecular techniques and biochemical analyses.
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Affiliation(s)
- Martina Zandl-Lang
- Division of General Pediatrics, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, 8036 Graz, Austria
| | - Barbara Plecko
- Division of General Pediatrics, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, 8036 Graz, Austria
| | - Harald Köfeler
- Core Facility Mass Spectrometry, ZMF, Medical University of Graz, 8036 Graz, Austria
- Correspondence:
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11
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Next Challenges for the Comprehensive Molecular Characterization of Complex Organic Mixtures in the Field of Sustainable Energy. Molecules 2022; 27:molecules27248889. [PMID: 36558021 PMCID: PMC9786309 DOI: 10.3390/molecules27248889] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
The conversion of lignocellulosic biomass by pyrolysis or hydrothermal liquefaction gives access to a wide variety of molecules that can be used as fuel or as building blocks in the chemical industry. For such purposes, it is necessary to obtain their detailed chemical composition to adapt the conversion process, including the upgrading steps. Petroleomics has emerged as an integral approach to cover a missing link in the investigation bio-oils and linked products. It relies on ultra-high-resolution mass spectrometry to attempt to unravel the contribution of many compounds in complex samples by a non-targeted approach. The most recent developments in petroleomics partially alter the discriminating nature of the non-targeted analyses. However, a peak referring to one chemical formula possibly hides a forest of isomeric compounds, which may present a large chemical diversity concerning the nature of the chemical functions. This identification of chemical functions is essential in the context of the upgrading of bio-oils. The latest developments dedicated to this analytical challenge will be reviewed and discussed, particularly by integrating ion source features and incorporating new steps in the analytical workflow. The representativeness of the data obtained by the petroleomic approach is still an important issue.
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12
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Role of Oxylipins in the Inflammatory-Related Diseases NAFLD, Obesity, and Type 2 Diabetes. Metabolites 2022; 12:metabo12121238. [PMID: 36557276 PMCID: PMC9788263 DOI: 10.3390/metabo12121238] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/03/2022] [Accepted: 12/04/2022] [Indexed: 12/13/2022] Open
Abstract
Oxygenated polyunsaturated fatty acids (oxylipins) are bioactive molecules established as important mediators during inflammation. Different classes of oxylipins have been found to have opposite effects, e.g., pro-inflammatory prostaglandins and anti-inflammatory resolvins. Production of the different classes of oxylipins occurs during distinct stages of development and resolution of inflammation. Chronic inflammation is involved in the progression of many pathophysiological conditions and diseases such as non-alcoholic fatty liver disease, insulin resistance, diabetes, and obesity. Determining oxylipin profiles before, during, and after inflammatory-related diseases could provide clues to the onset, development, and prevention of detrimental conditions. This review focusses on recent developments in our understanding of the role of oxylipins in inflammatory disease, and outlines novel technological advancements and approaches to study their action.
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13
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Hustin J, Kune C, Far J, Eppe G, Debois D, Quinton L, De Pauw E. Differential Kendrick's Plots as an Innovative Tool for Lipidomics in Complex Samples: Comparison of Liquid Chromatography and Infusion-Based Methods to Sample Differential Study. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:2273-2282. [PMID: 36378810 DOI: 10.1021/jasms.2c00232] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Lipidomics has developed rapidly over the past decade. Nontargeted lipidomics from biological samples remains a challenge due to the high structural diversity, the concentration range of lipids, and the complexity of biological samples. We introduce here the use of differential Kendrick's plots as a rapid visualization tool for a qualitative nontargeted analysis of lipids categories and classes from data generated by either liquid chromatography-mass spectrometry (LC-MS) or direct infusion (nESI-MS). Each lipid class is easily identified by comparison with the theoretical Kendrick plot pattern constructed from exact mass measurements and by using MSKendrickFilter, an in-house Python software. The lipids are identified with the LIPID MAPS database. In addition, in LC-MS, the software based on the Kendrick plots returns the retention time from all the lipids belonging to the same series. Lipid extracts from a yeast (Saccharomyces cerevisiae) are used as a model. An on/off case comparing Kendrick plots from two cell lines (prostate cancer cell lines treated or not with a DGAT2 inhibition) clearly shows the effect of the inhibition. Our study demonstrates the good performance of direct infusion as a fast qualitative screening method as well as for the analysis of chromatograms. A fast screening semiquantitative approach is also possible, while the targeted mode remains the golden standard for precise quantitative analysis.
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Affiliation(s)
- Justine Hustin
- Mass Spectrometry Laboratory, MolSys Research Unit, Department of Chemistry, University of Liège, Allée du Six Août 11 - Quartier Agora, 4000Liège, Belgium
| | - Christopher Kune
- Mass Spectrometry Laboratory, MolSys Research Unit, Department of Chemistry, University of Liège, Allée du Six Août 11 - Quartier Agora, 4000Liège, Belgium
| | - Johann Far
- Mass Spectrometry Laboratory, MolSys Research Unit, Department of Chemistry, University of Liège, Allée du Six Août 11 - Quartier Agora, 4000Liège, Belgium
| | - Gauthier Eppe
- Mass Spectrometry Laboratory, MolSys Research Unit, Department of Chemistry, University of Liège, Allée du Six Août 11 - Quartier Agora, 4000Liège, Belgium
| | | | - Loïc Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, Department of Chemistry, University of Liège, Allée du Six Août 11 - Quartier Agora, 4000Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research Unit, Department of Chemistry, University of Liège, Allée du Six Août 11 - Quartier Agora, 4000Liège, Belgium
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14
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Harlina PW, Maritha V, Musfiroh I, Huda S, Sukri N, Muchtaridi M. Possibilities of Liquid Chromatography Mass Spectrometry
(LC-MS)-Based Metabolomics and Lipidomics in the Authentication of Meat
Products: A Mini Review. Food Sci Anim Resour 2022; 42:744-761. [PMID: 36133639 PMCID: PMC9478982 DOI: 10.5851/kosfa.2022.e37] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
- Putri Widyanti Harlina
- Department of Food Industrial Technology,
Faculty of Agro-Industrial Technology, Universitas
Padjadjaran, Bandung 45363, Indonesia
- Corresponding author: Putri
Widyanti Harlina, Department of Food Industrial Technology, Faculty of
Agro-Industrial Technology, Universitas Padjadjaran, Bandung 45363, Indonesia,
Tel: +62-22-7798844, E-mail:
| | - Vevi Maritha
- Department of Pharmaceutical Analysis and
Medicinal Chemistry, Faculty of Pharmacy, Universitas
Padjadjaran, Bandung 45363, Indonesia
| | - Ida Musfiroh
- Department of Pharmaceutical Analysis and
Medicinal Chemistry, Faculty of Pharmacy, Universitas
Padjadjaran, Bandung 45363, Indonesia
| | - Syamsul Huda
- Department of Food Industrial Technology,
Faculty of Agro-Industrial Technology, Universitas
Padjadjaran, Bandung 45363, Indonesia
| | - Nandi Sukri
- Department of Food Industrial Technology,
Faculty of Agro-Industrial Technology, Universitas
Padjadjaran, Bandung 45363, Indonesia
| | - Muchtaridi Muchtaridi
- Department of Pharmaceutical Analysis and
Medicinal Chemistry, Faculty of Pharmacy, Universitas
Padjadjaran, Bandung 45363, Indonesia
- Corresponding author:
Muchtaridi Muchtaridi, Department of Pharmaceutical Analysis and Medicinal
Chemistry, Faculty of Pharmacy, Universitas Padjadjaran, Bandung 45363,
Indonesia, Tel: +62-22-8784288888 (ext. 3210), E-mail:
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15
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Paglia G, Smith AJ, Astarita G. Ion mobility mass spectrometry in the omics era: Challenges and opportunities for metabolomics and lipidomics. MASS SPECTROMETRY REVIEWS 2022; 41:722-765. [PMID: 33522625 DOI: 10.1002/mas.21686] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 01/17/2021] [Accepted: 01/17/2021] [Indexed: 06/12/2023]
Abstract
Researchers worldwide are taking advantage of novel, commercially available, technologies, such as ion mobility mass spectrometry (IM-MS), for metabolomics and lipidomics applications in a variety of fields including life, biomedical, and food sciences. IM-MS provides three main technical advantages over traditional LC-MS workflows. Firstly, in addition to mass, IM-MS allows collision cross-section values to be measured for metabolites and lipids, a physicochemical identifier related to the chemical shape of an analyte that increases the confidence of identification. Second, IM-MS increases peak capacity and the signal-to-noise, improving fingerprinting as well as quantification, and better defining the spatial localization of metabolites and lipids in biological and food samples. Third, IM-MS can be coupled with various fragmentation modes, adding new tools to improve structural characterization and molecular annotation. Here, we review the state-of-the-art in IM-MS technologies and approaches utilized to support metabolomics and lipidomics applications and we assess the challenges and opportunities in this growing field.
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Affiliation(s)
- Giuseppe Paglia
- School of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro (MB), Italy
| | - Andrew J Smith
- School of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro (MB), Italy
| | - Giuseppe Astarita
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, District of Columbia, USA
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16
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Moran-Garrido M, Camunas-Alberca SM, Gil-de-la Fuente A, Mariscal A, Gradillas A, Barbas C, Sáiz J. Recent developments in data acquisition, treatment and analysis with ion mobility-mass spectrometry for lipidomics. Proteomics 2022; 22:e2100328. [PMID: 35653360 DOI: 10.1002/pmic.202100328] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/29/2022] [Accepted: 05/30/2022] [Indexed: 11/08/2022]
Abstract
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 focusses 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. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- María Moran-Garrido
- Centre for Metabolomics and Bioanalysis (CEMBIO), Departamento de Química y Bioquímica, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, Madrid, Spain
| | - Sandra M Camunas-Alberca
- Centre for Metabolomics and Bioanalysis (CEMBIO), Departamento de Química y Bioquímica, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, Madrid, Spain
| | - Alberto Gil-de-la Fuente
- Centre for Metabolomics and Bioanalysis (CEMBIO), Departamento de Química y Bioquímica, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, Madrid, Spain.,Departamento de Tecnologías de la Información, Escuela Politécnica Superior, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Antonio Mariscal
- Centre for Metabolomics and Bioanalysis (CEMBIO), Departamento de Química y Bioquímica, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, Madrid, Spain.,Departamento de Tecnologías de la Información, Escuela Politécnica Superior, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Ana Gradillas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Departamento de Química y Bioquímica, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, Madrid, Spain
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Departamento de Química y Bioquímica, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, Madrid, Spain
| | - Jorge Sáiz
- Centre for Metabolomics and Bioanalysis (CEMBIO), Departamento de Química y Bioquímica, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, Madrid, Spain
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17
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Chen X, Yin Y, Luo M, Zhou Z, Cai Y, Zhu ZJ. Trapped ion mobility spectrometry-mass spectrometry improves the coverage and accuracy of four-dimensional untargeted lipidomics. Anal Chim Acta 2022; 1210:339886. [DOI: 10.1016/j.aca.2022.339886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/11/2022] [Accepted: 04/28/2022] [Indexed: 11/01/2022]
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18
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Rose BS, May JC, Picache JA, Codreanu SG, Sherrod SD, McLean JA. Improving confidence in lipidomic annotations by incorporating empirical ion mobility regression analysis and chemical class prediction. Bioinformatics 2022; 38:2872-2879. [PMID: 35561172 PMCID: PMC9306740 DOI: 10.1093/bioinformatics/btac197] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/22/2022] [Accepted: 03/29/2022] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Mass spectrometry-based untargeted lipidomics aims to globally characterize the lipids and lipid-like molecules in biological systems. Ion mobility increases coverage and confidence by offering an additional dimension of separation and a highly reproducible metric for feature annotation, the collision cross-section (CCS). RESULTS We present a data processing workflow to increase confidence in molecular class annotations based on CCS values. This approach uses class-specific regression models built from a standardized CCS repository (the Unified CCS Compendium) in a parallel scheme that combines a new annotation filtering approach with a machine learning class prediction strategy. In a proof-of-concept study using murine brain lipid extracts, 883 lipids were assigned higher confidence identifications using the filtering approach, which reduced the tentative candidate lists by over 50% on average. An additional 192 unannotated compounds were assigned a predicted chemical class. AVAILABILITY AND IMPLEMENTATION All relevant source code is available at https://github.com/McLeanResearchGroup/CCS-filter. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Bailey S Rose
- Department of Chemistry, Center for Innovative Technology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN 37235, USA
| | - Jody C May
- Department of Chemistry, Center for Innovative Technology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN 37235, USA
| | - Jaqueline A Picache
- Department of Chemistry, Center for Innovative Technology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN 37235, USA
| | - Simona G Codreanu
- Department of Chemistry, Center for Innovative Technology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN 37235, USA
| | - Stacy D Sherrod
- Department of Chemistry, Center for Innovative Technology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN 37235, USA
| | - John A McLean
- Department of Chemistry, Center for Innovative Technology, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN 37235, USA
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19
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Accelerating prototyping experiments for traveling wave structures for lossless ion manipulations. Talanta 2022; 244:123446. [PMID: 35397327 DOI: 10.1016/j.talanta.2022.123446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/27/2022] [Accepted: 04/02/2022] [Indexed: 11/22/2022]
Abstract
Traveling wave structures for lossless ion manipulation (TW-SLIM) has proven a valuable tool for the separation and study of gas-phase ions. Unfortunately, many of the traditional components of TW-SLIM experiments manifest practical and financial barriers to the technique's broad implementation. To this end, a series of technological innovations and methodologies are presented which enable for simplified SLIM experimentation and more rapid TW-SLIM prototyping. In addition to the use of multiple independent board sets that comprise the present SLIM system, we introduce a low-cost, multifunctional traveling wave generator to produce TW within the TW-SLIM. This square-wave producing unit proved effective in realizing TW-SLIM separations compared to traditional approaches. Maintaining a focus on lowering barriers to implementation, the present set of experiments explores the use of on-board injection (OBI) methods, which offer potential alternatives to ion funnel traps. These OBI techniques proved feasible and the ability of this simplified TW-SLIM platform to enhance ion accumulation was established. Further experimentation regarding ion accumulation revealed a complexity to ion accumulation within TW-SLIM that has yet to be expounded upon. Lastly, the ability of the presented TW-SLIM platform to store ions for extended periods (1 s) without significant loss (<10%) was demonstrated. The aforementioned experiments clearly establish the efficacy of a simplified TW-SLIM platform which promises to expand adoption and experimentation of the technique.
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20
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Vallejo DD, Rojas Ramírez C, Parson KF, Han Y, Gadkari VV, Ruotolo BT. Mass Spectrometry Methods for Measuring Protein Stability. Chem Rev 2022; 122:7690-7719. [PMID: 35316030 DOI: 10.1021/acs.chemrev.1c00857] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mass spectrometry is a central technology in the life sciences, providing our most comprehensive account of the molecular inventory of the cell. In parallel with developments in mass spectrometry technologies targeting such assessments of cellular composition, mass spectrometry tools have emerged as versatile probes of biomolecular stability. In this review, we cover recent advancements in this branch of mass spectrometry that target proteins, a centrally important class of macromolecules that accounts for most biochemical functions and drug targets. Our efforts cover tools such as hydrogen-deuterium exchange, chemical cross-linking, ion mobility, collision induced unfolding, and other techniques capable of stability assessments on a proteomic scale. In addition, we focus on a range of application areas where mass spectrometry-driven protein stability measurements have made notable impacts, including studies of membrane proteins, heat shock proteins, amyloidogenic proteins, and biotherapeutics. We conclude by briefly discussing the future of this vibrant and fast-moving area of research.
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Affiliation(s)
- Daniel D Vallejo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Carolina Rojas Ramírez
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kristine F Parson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yilin Han
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Varun V Gadkari
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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21
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Rontani JF. Use of Gas Chromatography-Mass Spectrometry Techniques (GC-MS, GC-MS/MS and GC-QTOF) for the Characterization of Photooxidation and Autoxidation Products of Lipids of Autotrophic Organisms in Environmental Samples. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27051629. [PMID: 35268730 PMCID: PMC8911584 DOI: 10.3390/molecules27051629] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/04/2022] [Accepted: 02/27/2022] [Indexed: 01/21/2023]
Abstract
This paper reviews applications of gas chromatography-mass spectrometry techniques for the characterization of photooxidation and autoxidation products of lipids of senescent phototrophic organisms. Particular attention is given to: (i) the selection of oxidation products that are sufficiently stable under environmental conditions and specific to each lipid class and degradation route; (ii) the description of electron ionization mass fragmentation of trimethylsilyl derivatives of these compounds; and (iii) the use of specific fragment ions for monitoring the oxidation of the main unsaturated lipid components of phototrophs. The techniques best geared for this task were gas chromatography-quadrupole-time of flight to monitor fragment ions with very high resolution and accuracy, and gas chromatography-tandem mass spectrometry to monitor very selective transitions in multiple reaction monitoring mode. The extent of the degradation processes can only be estimated if the oxidation products are unaffected by fast secondary oxidation reactions, as it is notably the case of ∆5-sterols, monounsaturated fatty acids, chlorophyll phytyl side-chain, and di- and triterpenoids. In contrast, the primary degradation products of highly branched isoprenoid alkenes possessing more than one trisubstituted double bond, alkenones, carotenoids and polyunsaturated fatty acids, appear to be too unstable with respect to secondary oxidation or other reactions to serve for quantification in environmental samples.
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Affiliation(s)
- Jean-François Rontani
- Mediterranean Institute of Oceanography (MIO), Aix Marseille University, Université de Toulon, CNRS, IRD, UM 110, 13288 Marseille, France
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22
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Koomen DC, May JC, McLean JA. Insights and prospects for ion mobility-mass spectrometry in clinical chemistry. Expert Rev Proteomics 2022; 19:17-31. [PMID: 34986717 PMCID: PMC8881341 DOI: 10.1080/14789450.2022.2026218] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
INTRODUCTION Ion mobility-mass spectrometry is an emerging technology in the clinical setting for high throughput and high confidence molecular characterization from complex biological samples. Ion mobility spectrometry can provide isomer separations on the basis of molecular structure, the ability of which is increasing through technological developments that afford enhanced resolving power. Integrating multiple separation dimensions, such as liquid chromatography-ion mobility-mass spectrometry (LC-IM-MS) provide dramatic enhancements in the mitigation of molecular interferences for high accuracy clinical measurements. AREAS COVERED Multidimensional separations with LC-IM-MS provide better selectivity and sensitivity in molecular analysis. Mass spectrometry imaging of tissues to inform spatial molecular distribution is improved by complementary ion mobility analyses. Biomarker identification in surgical environments is enhanced by intraoperative biochemical analysis with mass spectrometry and holds promise for integration with ion mobility spectrometry. New prospects in high resolving power ion mobility are enhancing analysis capabilities, such as distinguishing isomeric compounds. EXPERT OPINION Ion mobility-mass spectrometry holds many prospects for the field of isomer identification, molecular imaging, and intraoperative tumor margin delineation in clinical settings. These advantages are afforded while maintaining fast analysis times and subsequently high throughput. High resolving power ion mobility will enhance these advantages further, in particular for analyses requiring high confidence isobaric selectivity and detection.
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Affiliation(s)
- David C. Koomen
- Department of Chemistry, Center for Innovative Technology, Institute of Chemical Biology, Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Jody C. May
- Department of Chemistry, Center for Innovative Technology, Institute of Chemical Biology, Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - John A. McLean
- Department of Chemistry, Center for Innovative Technology, Institute of Chemical Biology, Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
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23
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Law KP, He W, Tao J, Zhang C. A Novel Approach to Characterize the Lipidome of Marine Archaeon Nitrosopumilus maritimus by Ion Mobility Mass Spectrometry. Front Microbiol 2021; 12:735878. [PMID: 34925256 PMCID: PMC8674956 DOI: 10.3389/fmicb.2021.735878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Archaea are differentiated from the other two domains of life by their biomolecular characteristics. One such characteristic is the unique structure and composition of their lipids. Characterization of the whole set of lipids in a biological system (the lipidome) remains technologically challenging. This is because the lipidome is innately complex, and not all lipid species are extractable, separable, or ionizable by a single analytical method. Furthermore, lipids are structurally and chemically diverse. Many lipids are isobaric or isomeric and often indistinguishable by the measurement of mass or even their fragmentation spectra. Here we developed a novel analytical protocol based on liquid chromatography ion mobility mass spectrometry to enhance the coverage of the lipidome and characterize the conformations of archaeal lipids by their collision cross-sections (CCSs). The measurements of ion mobility revealed the gas-phase ion chemistry of representative archaeal lipids and provided further insights into their attributions to the adaptability of archaea to environmental stresses. A comprehensive characterization of the lipidome of mesophilic marine thaumarchaeon, Nitrosopumilus maritimus (strain SCM1) revealed potentially an unreported phosphate- and sulfate-containing lipid candidate by negative ionization analysis. It was the first time that experimentally derived CCS values of archaeal lipids were reported. Discrimination of crenarchaeol and its proposed stereoisomer was, however, not achieved with the resolving power of the SYNAPT G2 ion mobility system, and a high-resolution ion mobility system may be required for future work. Structural and spectral libraries of archaeal lipids were constructed in non-vendor-specific formats and are being made available to the community to promote research of Archaea by lipidomics.
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Affiliation(s)
- Kai P Law
- Southern University of Science and Technology, SUSTech Academy for Advanced Interdisciplinary Studies, Shenzhen, China.,Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Wei He
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jianchang Tao
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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24
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Su B, Bettcher LF, Hsieh WY, Hornburg D, Pearson MJ, Blomberg N, Giera M, Snyder MP, Raftery D, Bensinger SJ, Williams KJ. A DMS Shotgun Lipidomics Workflow Application to Facilitate High-Throughput, Comprehensive Lipidomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2655-2663. [PMID: 34637296 PMCID: PMC8985811 DOI: 10.1021/jasms.1c00203] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Differential mobility spectrometry (DMS) is highly useful for shotgun lipidomic analysis because it overcomes difficulties in measuring isobaric species within a complex lipid sample and allows for acyl tail characterization of phospholipid species. Despite these advantages, the resulting workflow presents technical challenges, including the need to tune the DMS before every batch to update compensative voltages settings within the method. The Sciex Lipidyzer platform uses a Sciex 5500 QTRAP with a DMS (SelexION), an LC system configured for direction infusion experiments, an extensive set of standards designed for quantitative lipidomics, and a software package (Lipidyzer Workflow Manager) that facilitates the workflow and rapidly analyzes the data. Although the Lipidyzer platform remains very useful for DMS-based shotgun lipidomics, the software is no longer updated for current versions of Analyst and Windows. Furthermore, the software is fixed to a single workflow and cannot take advantage of new lipidomics standards or analyze additional lipid species. To address this multitude of issues, we developed Shotgun Lipidomics Assistant (SLA), a Python-based application that facilitates DMS-based lipidomics workflows. SLA provides the user with flexibility in adding and subtracting lipid and standard MRMs. It can report quantitative lipidomics results from raw data in minutes, comparable to the Lipidyzer software. We show that SLA facilitates an expanded lipidomics analysis that measures over 1450 lipid species across 17 (sub)classes. Lastly, we demonstrate that the SLA performs isotope correction, a feature that was absent from the original software.
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Affiliation(s)
- Baolong Su
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA
- UCLA Lipidomics Lab, University of California, Los Angeles, CA, USA
| | - Lisa F. Bettcher
- Department of Anesthesiology and Pain Medicine, Northwest Metabolomics Research Center, University of Washington, Seattle, WA, USA
| | - Wei-Yuan Hsieh
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel Hornburg
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Niek Blomberg
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333ZA Leiden, Netherlands
| | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333ZA Leiden, Netherlands
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Raftery
- Department of Anesthesiology and Pain Medicine, Northwest Metabolomics Research Center, University of Washington, Seattle, WA, USA
| | - Steven J. Bensinger
- UCLA Lipidomics Lab, University of California, Los Angeles, CA, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kevin J. Williams
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA
- UCLA Lipidomics Lab, University of California, Los Angeles, CA, USA
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26
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Köfeler HC, Ahrends R, Baker ES, Ekroos K, Han X, Hoffmann N, Holčapek M, Wenk MR, Liebisch G. Recommendations for good practice in MS-based lipidomics. J Lipid Res 2021; 62:100138. [PMID: 34662536 PMCID: PMC8585648 DOI: 10.1016/j.jlr.2021.100138] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 12/17/2022] Open
Abstract
In the last 2 decades, lipidomics has become one of the fastest expanding scientific disciplines in biomedical research. With an increasing number of new research groups to the field, it is even more important to design guidelines for assuring high standards of data quality. The Lipidomics Standards Initiative is a community-based endeavor for the coordination of development of these best practice guidelines in lipidomics and is embedded within the International Lipidomics Society. It is the intention of this review to highlight the most quality-relevant aspects of the lipidomics workflow, including preanalytics, sample preparation, MS, and lipid species identification and quantitation. Furthermore, this review just does not only highlights examples of best practice but also sheds light on strengths, drawbacks, and pitfalls in the lipidomic analysis workflow. While this review is neither designed to be a step-by-step protocol by itself nor dedicated to a specific application of lipidomics, it should nevertheless provide the interested reader with links and original publications to obtain a comprehensive overview concerning the state-of-the-art practices in the field.
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Affiliation(s)
- Harald C Köfeler
- Core Facility Mass Spectrometry, Medical University of Graz, Graz, Austria.
| | - Robert Ahrends
- Department for Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Esbo, Finland
| | - Xianlin Han
- Barshop Inst Longev & Aging Studies, Univ Texas Hlth Sci Ctr San Antonio, San Antonio, TX, USA
| | - Nils Hoffmann
- Center for Biotechnology, Universität Bielefeld, Bielefeld, Germany
| | - Michal Holčapek
- Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic
| | - Markus R Wenk
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, Singapore
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Regensburg, Germany.
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27
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Abstract
Native mass spectrometry (MS) is aimed at preserving and determining the native structure, composition, and stoichiometry of biomolecules and their complexes from solution after they are transferred into the gas phase. Major improvements in native MS instrumentation and experimental methods over the past few decades have led to a concomitant increase in the complexity and heterogeneity of samples that can be analyzed, including protein-ligand complexes, protein complexes with multiple coexisting stoichiometries, and membrane protein-lipid assemblies. Heterogeneous features of these biomolecular samples can be important for understanding structure and function. However, sample heterogeneity can make assignment of ion mass, charge, composition, and structure very challenging due to the overlap of tens or even hundreds of peaks in the mass spectrum. In this review, we cover data analysis, experimental, and instrumental advances and strategies aimed at solving this problem, with an in-depth discussion of theoretical and practical aspects of the use of available deconvolution algorithms and tools. We also reflect upon current challenges and provide a view of the future of this exciting field.
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Affiliation(s)
- Amber D Rolland
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States.,Materials Science Institute, University of Oregon, Eugene, Oregon 97403-1252, United States
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28
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Abstract
Lipids are natural substances found in all living organisms and involved in many biological functions. Imbalances in the lipid metabolism are linked to various diseases such as obesity, diabetes, or cardiovascular disease. Lipids comprise thousands of chemically distinct species making them a challenge to analyze because of their great structural diversity.Thanks to the technological improvements in the fields of chromatography, high-resolution mass spectrometry, and bioinformatics over the last years, it is now possible to perform global lipidomics analyses, allowing the concomitant detection, identification, and relative quantification of hundreds of lipid species. This review shall provide an insight into a general lipidomics workflow and its application in metabolic biomarker research.
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29
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Law KP, He W, Tao J, Zhang C. Characterization of the Exometabolome of Nitrosopumilus maritimus SCM1 by Liquid Chromatography-Ion Mobility Mass Spectrometry. Front Microbiol 2021; 12:658781. [PMID: 34276593 PMCID: PMC8281238 DOI: 10.3389/fmicb.2021.658781] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/04/2021] [Indexed: 11/13/2022] Open
Abstract
Marine Thaumarchaeota (formerly known as the marine group I archaea) have received much research interest in recent years since these chemolithoautotrophic organisms are abundant in the subsurface ocean and oxidize ammonium to nitrite, which makes them a major contributor to the marine carbon and nitrogen cycles. However, few studies have investigated the chemical composition of their exometabolome and their contributions to the pool of dissolved organic matter (DOM) in seawater. This study exploits the recent advances in ion mobility mass spectrometry (IM-MS) and integrates this instrumental capability with bioinformatics to reassess the exometabolome of a model ammonia-oxidizing archaeon, Nitrosopumilus maritimus strain SCM1. Our method has several advantages over the conventional approach using an Orbitrap or ion cyclotron resonance mass analyzer and allows assignments or annotations of spectral features to known metabolites confidently and indiscriminately, as well as distinction of biological molecules from background organics. Consistent with the results of a previous report, the SPE-extracted exometabolome of N. maritimus is dominated by biologically active nitrogen-containing metabolites, in addition to peptides secreted extracellularly. Cobalamin and associated intermediates, including α-ribazole and α-ribazole 5′-phosphate, are major components of the SPE-extracted exometabolome of N. maritimus. This supports the proposition that Thaumarchaeota have the capacity of de novo biosynthesizing cobalamin. Other biologically significant metabolites, such as agmatidine and medicagenate, predicted by genome screening are also detected, which indicates that Thaumarchaeota have remarkable metabolic potentials, underlining their importance in driving elemental cycles critical to biological processes in the ocean.
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Affiliation(s)
- Kai P Law
- SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China.,Shenzhen Key Laboratory of Marine Geo-Omics Research, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Wei He
- Shenzhen Key Laboratory of Marine Geo-Omics Research, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jianchang Tao
- Shenzhen Key Laboratory of Marine Geo-Omics Research, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Geo-Omics Research, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Shanghai Sheshan National Geophysical Observatory, Shanghai, China
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30
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Jin Y, Harvey TN, Bartosova Z, Hassani S, Bruheim P, Sandve SR, Vik JO. Diet and Life Stage-Associated Lipidome Remodeling in Atlantic Salmon. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:3787-3796. [PMID: 33754702 PMCID: PMC8041299 DOI: 10.1021/acs.jafc.0c07281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/05/2021] [Accepted: 03/15/2021] [Indexed: 05/07/2023]
Abstract
Salmon is an important source of long-chain highly unsaturated fatty acids (LC-HUFAs) such as 22:6n-3 [docosahexaenoic acid (DHA)]. In the present study, we conducted two identical experiments on salmon in freshwater (FW) and seawater (SW) stages, with a diet switch from fish oil (high in LC-HUFA) to vegetable oil (low in LC-HUFA) and vice versa. Our aim was to investigate the diet and life stage-specific features of lipid uptake (gut), processing (liver), and deposition (muscle). The lipid composition changed much faster in the gut of SW fish relative to FW fish, suggesting that the former had a higher rate of lipid absorption and transport. SW fish also had higher expression of phospholipid synthesis and lipoprotein formation genes in the gut, whereas FW fish had higher expression of lipid synthesis genes in the liver. All phospholipids except PC-44:12 and PE-44:12 were less abundant in SW, suggesting that SW fish have a higher requirement for DHA.
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Affiliation(s)
- Yang Jin
- Center
of Integrative Genetics (CIGENE), Norwegian
University of Life Sciences, 1430 Aas, Norway
| | - Thomas Nelson Harvey
- Center
of Integrative Genetics (CIGENE), Norwegian
University of Life Sciences, 1430 Aas, Norway
| | - Zdenka Bartosova
- Department
of Biotechnology and Food Science, Norwegian
University of Science and Technology, 7491 Trondheim, Norway
| | - Sahar Hassani
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Aas, Norway
| | - Per Bruheim
- Department
of Biotechnology and Food Science, Norwegian
University of Science and Technology, 7491 Trondheim, Norway
| | - Simen Rød Sandve
- Center
of Integrative Genetics (CIGENE), Norwegian
University of Life Sciences, 1430 Aas, Norway
| | - Jon Olav Vik
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Aas, Norway
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31
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Harlina PW, Ma M, Shahzad R. Quantification of Lipidomics Profiling using UPLC‐QE‐HESI‐ Lipid Analysis on the Salted Duck Egg Incorporated with Clove Extract. EUR J LIPID SCI TECH 2021. [DOI: 10.1002/ejlt.202000284] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Putri Widyanti Harlina
- Department of Food Technology, Faculty of Science and Technology Universitas Muhammadiyah Bandung Bandung West Java 40614 Indonesia
- National Research and Development Center for Egg Processing, College of Food Science and Technology Huazhong Agricultural University Wuhan Hubei 430070 P. R. China
| | - Meihu Ma
- National Research and Development Center for Egg Processing, College of Food Science and Technology Huazhong Agricultural University Wuhan Hubei 430070 P. R. China
| | - Raheel Shahzad
- Department of Biotechnology, Faculty of Science and Technology Universitas Muhammadiyah Bandung Bandung West Java 40614 Indonesia
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32
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Helmer PO, Nordhorn ID, Korf A, Behrens A, Buchholz R, Zubeil F, Karst U, Hayen H. Complementing Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry Imaging with Chromatography Data for Improved Assignment of Isobaric and Isomeric Phospholipids Utilizing Trapped Ion Mobility-Mass Spectrometry. Anal Chem 2021; 93:2135-2143. [PMID: 33416303 DOI: 10.1021/acs.analchem.0c03942] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Lipids, such for example the multifaceted category of glycerophospholipids (GP), play a major role in many biological processes. High-resolution mass spectrometry is able to identify these highly diverse lipid species in combination with fragmentation experiments (MS/MS) on the basis of the accurate m/z and fragmentation pattern. However, for the differentiation of isomeric lipids or isobaric interferences, more elaborate separation methods are required. Especially for imaging techniques, such as matrix-assisted laser desorption/ionization (MALDI)-MS imaging, the identification is often exclusively based on the accurate m/z. Fragmentation via MS/MS increases the confidence in lipid annotation in imaging approaches. However, this is sometimes not feasible due to insufficient sensitivity and significantly prolonged analysis time. The use of a separation dimension such as trapped ion mobility spectrometry (TIMS) after ionization strengthens the confidence of the identification based on the collision cross section (CCS). Since CCS libraries are limited, a tissue-specific database was initially generated using hydrophilic interaction liquid chromatography-TIMS-MS. Using this database, the identification of isomeric lipid classes as well as isobaric interferences in a lipid class was performed using a mouse spleen sample in a workflow described in this study. Besides a CCS-based identification as an additional identification criterion for GP in general, the focus was on the distinction of the isomeric GP classes phosphatidylglycerol and bis(monoacylglycero)phosphate, as well as the differentiation of possible isobaric interferences based on the formation of adducts by MALDI-TIMS-MS imaging on a molecular level.
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Affiliation(s)
- Patrick O Helmer
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 30, Münster 48149, Germany
| | - Ilona D Nordhorn
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 30, Münster 48149, Germany
| | - Ansgar Korf
- Bruker Daltonik GmbH, Fahrenheitstraße 4, Bremen 28359, Germany
| | - Arne Behrens
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 30, Münster 48149, Germany
| | - Rebecca Buchholz
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 30, Münster 48149, Germany
| | - Florian Zubeil
- Bruker Daltonik GmbH, Fahrenheitstraße 4, Bremen 28359, Germany
| | - Uwe Karst
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 30, Münster 48149, Germany
| | - Heiko Hayen
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 30, Münster 48149, Germany
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33
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Wormwood Moser KL, Van Aken G, DeBord D, Hatcher NG, Maxon L, Sherman M, Yao L, Ekroos K. High-defined quantitative snapshots of the ganglioside lipidome using high resolution ion mobility SLIM assisted shotgun lipidomics. Anal Chim Acta 2021; 1146:77-87. [DOI: 10.1016/j.aca.2020.12.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/03/2020] [Accepted: 12/14/2020] [Indexed: 10/22/2022]
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34
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Masike K, Stander MA, de Villiers A. Recent applications of ion mobility spectrometry in natural product research. J Pharm Biomed Anal 2021; 195:113846. [PMID: 33422832 DOI: 10.1016/j.jpba.2020.113846] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/08/2020] [Accepted: 12/08/2020] [Indexed: 12/15/2022]
Abstract
Ion mobility spectrometry (IMS) is a rapid separation technique capable of extracting complementary structural information to chromatography and mass spectrometry (MS). IMS, especially in combination with MS, has experienced inordinate growth in recent years as an analytical technique, and elicited intense interest in many research fields. In natural product analysis, IMS shows promise as an additional tool to enhance the performance of analytical methods used to identify promising drug candidates. Potential benefits of the incorporation of IMS into analytical workflows currently used in natural product analysis include the discrimination of structurally similar secondary metabolites, improving the quality of mass spectral data, and the use of mobility-derived collision cross-section (CCS) values as an additional identification criterion in targeted and untargeted analyses. This review aims to provide an overview of the application of IMS to natural product analysis over the last six years. Instrumental aspects and the fundamental background of IMS will be briefly covered, and recent applications of the technique for natural product analysis will be discussed to demonstrate the utility of the technique in this field.
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Affiliation(s)
- Keabetswe Masike
- Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Maria A Stander
- Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa; Central Analytical Facility, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - André de Villiers
- Department of Chemistry and Polymer Science, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
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35
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Rose BS, Leaptrot KL, Harris RA, Sherrod SD, May JC, McLean JA. High Confidence Shotgun Lipidomics Using Structurally Selective Ion Mobility-Mass Spectrometry. Methods Mol Biol 2021; 2306:11-37. [PMID: 33954937 PMCID: PMC10127451 DOI: 10.1007/978-1-0716-1410-5_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ion mobility (IM) is a gas phase separation strategy that can either supplement or serve as a high-throughput alternative to liquid chromatography (LC) in shotgun lipidomics. Incorporating the IM dimension in untargeted lipidomics workflows can help resolve isomeric lipids, and the collision cross section (CCS) values obtained from the IM measurements can provide an additional molecular descriptor to increase lipid identification confidence. This chapter provides a broad overview of an untargeted ion mobility-mass spectrometry (IM-MS) workflow using a commercial drift tube ion mobility-quadrupole-time-of-flight mass spectrometer (IM-QTOF) for high confidence lipidomics.
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Affiliation(s)
- Bailey S Rose
- Center for Innovative Technology, Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Katrina L Leaptrot
- Center for Innovative Technology, Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Rachel A Harris
- Center for Innovative Technology, Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Stacy D Sherrod
- Center for Innovative Technology, Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Jody C May
- Center for Innovative Technology, Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - John A McLean
- Center for Innovative Technology, Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA.
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
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36
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Abstract
Over the last few decades, MS-based lipidomics has emerged as a powerful tool to study lipids in biological systems. This success is driven by the constant demand for complete and reliable data. The improvement of MS-based lipidomics will continue to be dependent on the advances in the technology of mass spectrometry and related techniques including separation and bioinformatics, and more importantly, on gaining insight into the knowledge of lipid chemistry essential to develop methodology for lipid analysis. It is hoped that the protocols in this book, collected from experts in their fields, can offer the beginner and the advanced user alike, useful tips toward successful lipidomic analysis.
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Affiliation(s)
- Fong-Fu Hsu
- Mass Spectrometry Resource, Division of Endocrinology, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
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37
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High-coverage lipidomics for functional lipid and pathway analyses. Anal Chim Acta 2020; 1147:199-210. [PMID: 33485579 DOI: 10.1016/j.aca.2020.11.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 11/10/2020] [Accepted: 11/18/2020] [Indexed: 12/19/2022]
Abstract
Rapid advances in front-end separation approaches and analytical technologies have accelerated the development of lipidomics, particularly in terms of increasing analytical coverage to encompass an expanding repertoire of lipids within a single analytical approach. Developments in lipid pathway analysis, however, have somewhat lingered behind, primarily due to (1) the lack of coherent alignment between lipid identifiers in common databases versus that generated from experiments, owing to the differing structural resolution of lipids at molecular level that is specific to the analytical approaches adopted by various laboratories; (2) the immense complexity of lipid metabolic relationships that may entail head group changes, fatty acyls modifications of various forms (e.g. elongation, desaturation, oxidation), as well as active remodeling that demands a multidimensional, panoramic view to take into account all possibilities in lipid pathway analyses. Herein, we discuss current efforts undertaken to address these challenges, as well as alternative form of "pathway analyses" that may be particularly useful for uncovering functional lipid interactions under different biological contexts. Consolidating lipid pathway analyses will be indispensable in facilitating the transition of lipidomics from its prior role of phenotype validation to a hypothesis-generating tool that uncovers novel molecular targets to drive downstream mechanistic pursuits under biomedical settings.
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38
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Gong M, Wei W, Hu Y, Jin Q, Wang X. Structure determination of conjugated linoleic and linolenic acids. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1153:122292. [PMID: 32755819 DOI: 10.1016/j.jchromb.2020.122292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/23/2020] [Accepted: 07/27/2020] [Indexed: 12/14/2022]
Abstract
Conjugated linoleic and linolenic acids (CLA and CLnA) can be found in dairy, ruminant meat and oilseeds, these types of unsaturated fatty acids consist of various positional and geometrical isomers, and have demonstrated health-promoting potential for human beings. Extensive reviews have reported the physiological effects of CLA, CLnA, while little is known regarding their isomer-specific effects. However, the isomers are difficult to identify, owing to (i) the similar retention time in common chromatographic methods; and (ii) the isomers are highly sensitive to high temperature, pH changes, and oxidation. The uncertainties in molecular structure have hindered investigations on the physiological effects of CLA and CLnA. Therefore, this review presents a summary of the currently available technologies for the structural determination of CLA and CLnA, including the presence confirmation, double bond position determination, and the potential stereo-isomer determination. Special focus has been projected to the novel techniques for structure determination of CLA and CLnA. Some possible future directions are also proposed.
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Affiliation(s)
- Mengyue Gong
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
| | - Wei Wei
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
| | - Yulin Hu
- Department of Chemical and Biochemical Engineering, University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Qingzhe Jin
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
| | - Xingguo Wang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China.
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39
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Helmer PO, Behrens A, Rudt E, Karst U, Hayen H. Hydroperoxylated vs Dihydroxylated Lipids: Differentiation of Isomeric Cardiolipin Oxidation Products by Multidimensional Separation Techniques. Anal Chem 2020; 92:12010-12016. [PMID: 32867498 DOI: 10.1021/acs.analchem.0c02605] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In recent years, cardiolipin (CL) oxidation products were recognized as potential markers for mitochondrial dysfunction in conjunction with age related diseases. The analysis of oxidized CL requires powerful analysis techniques due to high structural diversity. In addition, low concentrations of partly labile compounds pose a special challenge, supplemented by the occurrence of isomeric compounds, e.g., hydroperoxylated vs dihydroxylated products. Therefore, we present a hyphenated method based on liquid chromatography coupled to trapped ion mobility spectrometry (TIMS) for separation and tandem mass spectrometry (MS/MS) for structural characterization. This enables comprehensive analysis of an artificially oxidized CL extract of bovine heart. Isomeric oxidation products could be differentiated by mobility-resolved MS/MS fragmentation experiments. Our developed method could help to better understand the physiological role of oxidized CL.
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Affiliation(s)
- Patrick O Helmer
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstr. 30, 48149 Münster, Germany
| | - Arne Behrens
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstr. 30, 48149 Münster, Germany
| | - Edward Rudt
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstr. 30, 48149 Münster, Germany
| | - Uwe Karst
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstr. 30, 48149 Münster, Germany
| | - Heiko Hayen
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstr. 30, 48149 Münster, Germany
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40
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Picache JA, May JC, McLean JA. Chemical Class Prediction of Unknown Biomolecules Using Ion Mobility-Mass Spectrometry and Machine Learning: Supervised Inference of Feature Taxonomy from Ensemble Randomization. Anal Chem 2020; 92:10759-10767. [DOI: 10.1021/acs.analchem.0c02137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jaqueline A. Picache
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jody C. May
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - John A. McLean
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
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41
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Morsa D, Hanozin E, Eppe G, Quinton L, Gabelica V, Pauw ED. Effective Temperature and Structural Rearrangement in Trapped Ion Mobility Spectrometry. Anal Chem 2020; 92:4573-4582. [DOI: 10.1021/acs.analchem.9b05850] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Denis Morsa
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège 4000, Belgium
| | - Emeline Hanozin
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège 4000, Belgium
| | - Gauthier Eppe
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège 4000, Belgium
| | - Loïc Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège 4000, Belgium
| | - Valérie Gabelica
- University of Bordeaux, INSERM and CNRS, Laboratoire Acides Nucléiques: Régulations Naturelles et Artificielles (ARNA, U1212, UMR5320), IECB, Pessac 33600, France
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège 4000, Belgium
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42
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Fenclova M, Stranska-Zachariasova M, Benes F, Novakova A, Jonatova P, Kren V, Vitek L, Hajslova J. Liquid chromatography-drift tube ion mobility-mass spectrometry as a new challenging tool for the separation and characterization of silymarin flavonolignans. Anal Bioanal Chem 2020; 412:819-832. [PMID: 31919606 DOI: 10.1007/s00216-019-02274-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/29/2019] [Accepted: 11/11/2019] [Indexed: 12/30/2022]
Abstract
Silymarin, milk thistle (Silybum marianum) extract, contains a mixture of mostly isomeric bioactive flavonoids and flavonolignans that are extensively studied, especially for their possible liver-protective and anticancer effects. Because of the differing bioactivities of individual isomeric compounds, characterization of their proportion in a mixture is highly important for predicting its effect on health. However, because of silymarin's complexity, this is hardly feasible by common analytical techniques. In this work, ultraperformance liquid chromatography coupled with drift tube ion mobility spectrometry and quadrupole time-of-flight mass spectrometry was used. Eleven target silymarin compounds (taxifolin, isosilychristin, silychristins A and B, silydianin, silybins A and B, 2,3-cis-silybin B, isosilybins A and B and 2,3-dehydrosilybin) and five unknown flavonolignan isomers detected in the milk thistle extract were fully separated in a 14.5-min analysis run. All the compounds were characterized on the basis of their accurate mass, retention time, drift time, collision cross section and fragmentation spectra. The quantitative approach based on evaluation of the ion mobility data demonstrated lower detection limits, an extended linear range and total separation of interferences from the compounds of interest compared with the traditional approach based on evaluation of liquid chromatography-quadrupole time-of-flight mass spectrometry data. The following analysis of a batch of milk thistle-based food supplements revealed significant variability in the silymarin pattern, especially in the content of silychristin A and silybins A and B. This newly developed method might have high application potential, especially for the characterization of materials intended for bioactivity studies in which information on the exact silymarin composition plays a crucial role. Graphical Abstract.
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Affiliation(s)
- Marie Fenclova
- Department of Food Analysis and Nutrition, University of Chemistry and Technology, Technická 3, 16628, Prague 6, Czech Republic
| | - Milena Stranska-Zachariasova
- Department of Food Analysis and Nutrition, University of Chemistry and Technology, Technická 3, 16628, Prague 6, Czech Republic.
| | - Frantisek Benes
- Department of Food Analysis and Nutrition, University of Chemistry and Technology, Technická 3, 16628, Prague 6, Czech Republic
| | - Alena Novakova
- Department of Food Analysis and Nutrition, University of Chemistry and Technology, Technická 3, 16628, Prague 6, Czech Republic
| | - Petra Jonatova
- Department of Food Analysis and Nutrition, University of Chemistry and Technology, Technická 3, 16628, Prague 6, Czech Republic
| | - Vladimir Kren
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Libor Vitek
- Institute of Medical Biochemistry and Laboratory Diagnostics and 4th Department of Internal Medicine, 1st Faculty of Medicine and Faculty General Hospital, Charles University, Katerinska 32, 12108, Prague 2, Czech Republic
| | - Jana Hajslova
- Department of Food Analysis and Nutrition, University of Chemistry and Technology, Technická 3, 16628, Prague 6, Czech Republic
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43
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Morris CB, Poland JC, May JC, McLean JA. Fundamentals of Ion Mobility-Mass Spectrometry for the Analysis of Biomolecules. Methods Mol Biol 2020; 2084:1-31. [PMID: 31729651 DOI: 10.1007/978-1-0716-0030-6_1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ion mobility-mass spectrometry (IM-MS) combines complementary size- and mass-selective separations into a single analytical platform. This chapter provides context for both the instrumental arrangements and key application areas that are commonly encountered in bioanalytical settings. New advances in these high-throughput strategies are described with description of complementary informatics tools to effectively utilize these data-intensive measurements. Rapid separations such as these are especially important in systems, synthetic, and chemical biology in which many small molecules are transient and correspond to various biological classes for integrated omics measurements. This chapter highlights the fundamentals of IM-MS and its applications toward biomolecular separations and discusses methods currently being used in the fields of proteomics, lipidomics, and metabolomics.
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Affiliation(s)
- Caleb B Morris
- Department of Chemistry, Center for Innovative Technology, Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA.,Vanderbilt-Ingram Cancer Center, Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN, USA
| | - James C Poland
- Department of Chemistry, Center for Innovative Technology, Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA.,Vanderbilt-Ingram Cancer Center, Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN, USA
| | - Jody C May
- Department of Chemistry, Center for Innovative Technology, Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA.,Vanderbilt-Ingram Cancer Center, Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN, USA
| | - John A McLean
- Department of Chemistry, Center for Innovative Technology, Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA. .,Vanderbilt-Ingram Cancer Center, Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN, USA.
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44
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King AM, Trengove RD, Mullin LG, Rainville PD, Isaac G, Plumb RS, Gethings LA, Wilson ID. Rapid profiling method for the analysis of lipids in human plasma using ion mobility enabled-reversed phase-ultra high performance liquid chromatography/mass spectrometry. J Chromatogr A 2020; 1611:460597. [DOI: 10.1016/j.chroma.2019.460597] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 09/19/2019] [Accepted: 10/03/2019] [Indexed: 12/22/2022]
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45
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Wu Z, Bagarolo GI, Thoröe-Boveleth S, Jankowski J. "Lipidomics": Mass spectrometric and chemometric analyses of lipids. Adv Drug Deliv Rev 2020; 159:294-307. [PMID: 32553782 DOI: 10.1016/j.addr.2020.06.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 06/03/2020] [Accepted: 06/06/2020] [Indexed: 01/01/2023]
Abstract
Lipids are ubiquitous in the human organism and play essential roles as components of cell membranes and hormones, for energy storage or as mediators of cell signaling pathways. As crucial mediators of the human metabolism, lipids are also involved in metabolic diseases, cardiovascular and renal diseases, cancer and/or hepatological and neurological disorders. With rapidly growing evidence supporting the impact of lipids on both the genesis and progression of these diseases as well as patient wellbeing, the characterization of the human lipidome has gained high interest and importance in life sciences and clinical diagnostics within the last 15 years. This is mostly due to technically advanced molecular identification and quantification methods, mainly based on mass spectrometry. Mass spectrometry has become one of the most powerful tools for the identification of lipids. New lipidic mediators or biomarkers of diseases can be analysed by state-of-the art mass spectrometry techniques supported by sophisticated bioinformatics and biostatistics. The lipidomic approach has developed dramatically in the realm of life sciences and clinical diagnostics due to the available mass spectrometric methods and in particular due to the adaptation of biostatistical methods in recent years. Therefore, the current knowledge of lipid extraction methods, mass-spectrometric approaches, biostatistical data analysis, including workflows for the interpretation of lipidomic high-throughput data, are reviewed in this manuscript.
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Affiliation(s)
- Zhuojun Wu
- Institute for Molecular Cardiovascular Research, University Hospital RWTH Aachen, Aachen, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Giulia Ilaria Bagarolo
- Institute for Molecular Cardiovascular Research, University Hospital RWTH Aachen, Aachen, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Sven Thoröe-Boveleth
- Institute for Molecular Cardiovascular Research, University Hospital RWTH Aachen, Aachen, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Joachim Jankowski
- Institute for Molecular Cardiovascular Research, University Hospital RWTH Aachen, Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; School for Cardiovascular Diseases, Maastricht University, Universiteitssingel 50, Maastricht, The Netherlands.
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46
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Vissers JPC, McCullagh M. An Analytical Perspective on Protein Analysis and Discovery Proteomics by Ion Mobility-Mass Spectrometry. Methods Mol Biol 2020; 2084:161-178. [PMID: 31729660 DOI: 10.1007/978-1-0716-0030-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ion mobility combined with mass spectrometry (IM-MS) is a powerful technique for the analysis of biomolecules and complex mixtures. This chapter reviews the current state-of-the-art in ion mobility technology and its application to biology, protein analysis, and quantitative discovery proteomics in particular, from an analytical perspective. IM-MS can be used as a technique to separate mixtures, to determine structural information (rotationally averaged cross-sectional area) and to enhance MS duty cycle and sensitivity. Moreover, IM-MS is ideally suited for hyphenating with liquid chromatography, or other front-end separation techniques such as, GC, microcolumn LC, capillary electrophoresis, and direct analysis, including MALDI and DESI, providing an semiorthogonal layer of separation, which affords the more unambiguous and confident detection of a wide range of analytes. To illustrate these enhancements, as well as recent developments, the principle of in-line IM separation and hyphenation to orthogonal acceleration time-of-flight mass spectrometers are discussed, in addition to the enhancement of biophysical MS-based analysis using typical proteomics and related application examples.
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47
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Abstract
Lipidomics is a rapidly growing field that enables the characterization of the entire lipidome in cells, tissues, or an organism. Changes in lipid metabolism and homeostasis caused by different disease states or drug treatments can be probed by lipidomics experiments, which can aid our understanding of normal physiology and disease pathology at the molecular level. While current technologies using liquid chromatography coupled with high-resolution mass spectrometry have greatly increased coverage of the lipidome, there are still limitations in resolving the large number of lipid species with similar masses in a narrow mass window. We recently reported that two orthogonal separation techniques, hydrophilic interaction liquid chromatography (HILIC) and ion mobility (IM), enhance the resolution of lipid species based on headgroup polarity and gas-phase size and shape, respectively, of various classes of glycerolipids, glycolipids, phospholipids, and sphingolipids. Here we describe the application of our HILIC-IM-MS lipidomics protocol to the analysis of lipid extracts derived from either tissues or cells, to identify significant changes in the lipidome in response to an internal or external stimulus, such as exposure to environmental chemicals.
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Affiliation(s)
- Amy Li
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Kelly M Hines
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Libin Xu
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA.
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48
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Metabolomic Profiling of Adherent Mammalian Cells In Situ by LAESI-MS with Ion Mobility Separation. Methods Mol Biol 2020; 2084:235-244. [PMID: 31729665 DOI: 10.1007/978-1-0716-0030-6_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Ambient ionization-based mass spectrometry (MS) methods coupled with ion mobility separation (IMS) have emerged as promising approaches for high-throughput in situ analysis for biomedical to environmental applications. These methods are capable of direct profiling and molecular imaging of metabolites, lipids, peptides, and xenobiotics from biological tissues with minimal sample preparation. Furthermore, employing IMS within the workflow improves the molecular coverage, resolves isobaric species, and improves biomolecule identifications through accurate collision cross section measurements. Laser ablation electrospray ionization (LAESI)-MS coupled with IMS has been successful in profiling and molecular imaging of small biomolecules directly from biological tissues and single cells. Herein, we describe a protocol for the direct analysis of adherent mammalian cells with limited perturbations by LAESI-IMS-MS. A benefit of IMS is that within the same LAESI acquisition, the spectral features related to the ESI background, washing buffer, and cell signal can be extracted and isolated separately.
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49
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Li A, Garimella SVB, Ibrahim YM. A simulation study of the influence of the traveling wave patterns on ion mobility separations in structures for lossless ion manipulations. Analyst 2019; 145:240-248. [PMID: 31746829 DOI: 10.1039/c9an01509d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Probing molecular properties in the gas phase requires the integration of complementary ion manipulation approaches such as ion mobility spectrometry. Structures for lossless ion manipulations (SLIM) have recently been developed to perform ultra-high resolution ion mobility separations using traveling waves as well as providing other advanced capabilities. Despite its success, the design aspects of SLIM have not been fully explored and remained largely unchanged. Here, we report on a computational study using SIMION simulations of a number of traveling wave (TW) patterns that can be used in SLIM. The TW pattern used in the current SLIM device is a set of 8 electrodes where, at any time, 4 electrodes are held at high voltage (i.e., 1111), while the other 4 electrodes are held at low voltage (i.e., 0000), forming one micro-trapping region of 11110000 pattern. Ion trajectory simulations demonstrated the feasibility to simplify the 8-electrode set to a shorter pattern (e.g., 6-electrode or 4-electrode set) while maintaining or improving the performance. The RF and TW amplitudes, guard voltage, and TW speed were optimized subsequently on the symmetric patterns of the 4-, 6-, and 8-electrode sets to further improve the performance. The resolution, peak broadening, peak capacity, and peak generation rate of each pattern were evaluated, showing that the 111000 pattern of the 6-electrode set has comparable performance to the current 11110000 pattern and is always better than the 1100 pattern. This work provides insight into the feasibility for simplification and modification of the TW configuration in SLIM and other traveling wave devices.
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Affiliation(s)
- Ailin Li
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
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50
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Li L, Zhong S, Shen X, Li Q, Xu W, Tao Y, Yin H. Recent development on liquid chromatography-mass spectrometry analysis of oxidized lipids. Free Radic Biol Med 2019; 144:16-34. [PMID: 31202785 DOI: 10.1016/j.freeradbiomed.2019.06.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/21/2019] [Accepted: 06/05/2019] [Indexed: 12/13/2022]
Abstract
Polyunsaturated fatty acids (PUFAs) in the cellular membrane can be oxidized by various enzymes or reactive oxygen species (ROS) to form many oxidized lipids. These metabolites are highly bioactive, participating in a variety of physiological and pathophysiological processes. Mass spectrometry (MS), coupled with Liquid Chromatography, has been increasingly recognized as an indispensable tool for the analysis of oxidized lipids due to its excellent sensitivity and selectivity. We will give an update on the understanding of the molecular mechanisms related to generation of various oxidized lipids and recent progress on the development of LC-MS in the detection of these bioactive lipids derived from fatty acids, cholesterol esters, and phospholipids. The purpose of this review is to provide an overview of the formation mechanisms and technological advances in LC-MS for the study of oxidized lipids in human diseases, and to shed new light on the potential of using oxidized lipids as biomarkers and mechanistic clues of pathogenesis related to lipid metabolism. The key technical problems associated with analysis of oxidized lipids and challenges in the field will also discussed.
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Affiliation(s)
- Luxiao Li
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, 200031, China; University of Chinese Academy of Sciences, CAS, Beijing, 100049, China
| | - Shanshan Zhong
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, 200031, China; University of Chinese Academy of Sciences, CAS, Beijing, 100049, China
| | - Xia Shen
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, 200031, China; University of Chinese Academy of Sciences, CAS, Beijing, 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 200031, China
| | - Qiujing Li
- Department of Pharmacy, Zhangzhou Health Vocational College, Zhangzhou, 363000, China
| | - Wenxin Xu
- Department of Medical Technology, Zhangzhou Health Vocational College, Zhangzhou, 363000, China
| | - Yongzhen Tao
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, 200031, China
| | - Huiyong Yin
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, 200031, China; University of Chinese Academy of Sciences, CAS, Beijing, 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 200031, China; Key Laboratory of Food Safety Risk Assessment, Ministry of Health, Beijing, 100000, China.
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