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Kwantwi-Barima P, Hollerbach AL, Attah IK, Norheim RV, Ibrahim YM. Ion Mobility Separations Using Cocentric Architecture. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1576-1583. [PMID: 38859729 DOI: 10.1021/jasms.4c00163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Ion mobility separations, especially using drift tube ion mobility spectrometers, are usually performed in linear channels, which can have a large footprint when extended to achieve higher resolving powers. In this work, we explored the performance of an ion mobility device with a curved architecture, which can have a more compact form. The cocentric ion mobility spectrometer (CoCIMS) manipulates ions between two cocentric surfaces containing a serpentine track. The mobility separation inside the CoCIMS is achieved using traveling waveforms (TWs). We initially evaluated the device using ion trajectory simulations using SIMION, which indicated that when ions traveled circularly inside the CoCIMS they resulted in similar resolving powers and transmitted m/z range as traveling in a straight path. We then performed experimental validation of the CoCIMS in conjunction with a TOF MS. The CoCIMS was made of two flexible printed circuit board materials folded into cocentric cylinders separated by a gap of 2.8 mm. The device was about 50 mm diameter ×152 mm long and provided 1.846 m of serpentine path length. Three sets of mixtures (Agilent tune mixture, tetraalkylammonium salts, and an eight-peptide mixture) and four traveling waveform profiles (square, sine, triangle, and sawtooth) were used. The sawtooth TW profile produced a slightly higher resolving power for the Agilent tuning mixture and tetraalkylammonium ions. The average resolving power for Agilent tune mixture ions ranged from 37 (using sawtooth TW) to 27 (using square TW). The average resolving powers ranged from 45 (sawtooth TW) to 31 (square TW) for tetraalkylammonium ions. The resolving power of the peptide mixture ions was similar among the four TW profiles and ranged from 51 to 56. The average percent error in TWCCS for the peptide mixture ions was about 0.4%. The new device showed promising results, but improvements are needed to further increase the resolving power.
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Affiliation(s)
- Pearl Kwantwi-Barima
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Adam L Hollerbach
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Isaac K Attah
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Randolph V Norheim
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Yehia M Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
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2
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Lundy DJ, Szomolay B, Liao CT. Systems Approaches to Cell Culture-Derived Extracellular Vesicles for Acute Kidney Injury Therapy: Prospects and Challenges. FUNCTION 2024; 5:zqae012. [PMID: 38706963 PMCID: PMC11065115 DOI: 10.1093/function/zqae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/02/2024] [Accepted: 03/05/2024] [Indexed: 05/07/2024] Open
Abstract
Acute kidney injury (AKI) is a heterogeneous syndrome, comprising diverse etiologies of kidney insults that result in high mortality and morbidity if not well managed. Although great efforts have been made to investigate underlying pathogenic mechanisms of AKI, there are limited therapeutic strategies available. Extracellular vesicles (EV) are membrane-bound vesicles secreted by various cell types, which can serve as cell-free therapy through transfer of bioactive molecules. In this review, we first overview the AKI syndrome and EV biology, with a particular focus on the technical aspects and therapeutic application of cell culture-derived EVs. Second, we illustrate how multi-omic approaches to EV miRNA, protein, and genomic cargo analysis can yield new insights into their mechanisms of action and address unresolved questions in the field. We then summarize major experimental evidence regarding the therapeutic potential of EVs in AKI, which we subdivide into stem cell and non-stem cell-derived EVs. Finally, we highlight the challenges and opportunities related to the clinical translation of animal studies into human patients.
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Affiliation(s)
- David J Lundy
- Graduate Institute of Biomedical Materials & Tissue Engineering, Taipei Medical University, Taipei 235603, Taiwan
- International PhD Program in Biomedical Engineering, Taipei Medical University, Taipei 235603, Taiwan
- Center for Cell Therapy, Taipei Medical University Hospital, Taipei 110301, Taiwan
| | - Barbara Szomolay
- Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
| | - Chia-Te Liao
- Division of Nephrology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
- Division of Nephrology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Research Center of Urology and Kidney, Taipei Medical University, Taipei 110, Taiwan
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3
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Harris RA, May JC, Harvey SR, Wysocki VH, McLean JA. Evaluation of Surface-Induced Dissociation Ion Mobility-Mass Spectrometry for Lipid Structural Characterization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:214-223. [PMID: 38215279 DOI: 10.1021/jasms.3c00319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2024]
Abstract
The complexity of the lipidome has necessitated the development of novel analytical approaches for the identification and structural analysis of morphologically diverse classes of lipids. At this time, a variety of dissociation techniques have been utilized to probe lipid decomposition pathways in search of structurally diagnostic fragment ions. Here, we investigate the application of surface-induced dissociation (SID), a fragmentation technique that imparts energy to the target molecule via collision with a coated surface, for the fragmentation of seven lipids across four major lipid subclasses. We have developed a tuning methodology for guiding the efficient operation of a previously developed custom SID device for molecules as small as ca. 300 Da with ion mobility analysis of the fragmentation products. SID fragmentation of the various lipids analyzed was found to generate fragment ions similar to those observed in CID spectra, but fragment ion lab frame onset energies were lower in SID due to the higher energy deposition via a more massive target. For the largest lipid evaluated (cardiolipin 18:1), SID produced chain fragment ions, which yielded analytically useful information regarding the composition of the acyl tails. Ion mobility provided an orthogonal dimension of separation and aided in assigning product ions to their precursors. Overall, the combination of SID and IM-MS is another potential methodology in the analytical toolkit for lipid structural analysis.
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Affiliation(s)
- Rachel A Harris
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, 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 University, Nashville, Tennessee 37235, United States
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, 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 University, Nashville, Tennessee 37235, United States
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Kwantwi-Barima P, Garimella SVB, Attah IK, Zheng X, Ibrahim YM, Smith RD. Accumulation of Large Ion Populations with High Ion Densities and Effects Due to Space Charge in Traveling Wave-Based Structures for Lossless Ion Manipulations (SLIM) IMS-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:365-377. [PMID: 38175933 PMCID: PMC10853970 DOI: 10.1021/jasms.3c00389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/19/2023] [Accepted: 12/13/2023] [Indexed: 01/06/2024]
Abstract
The accumulation of very large ion populations in traveling wave (TW)-based Structures for Lossless ion Manipulations (SLIM) has been studied to better understand aspects of "in-SLIM" ion accumulation, and particularly its use in conjunction with ion mobility spectrometry (IMS). A linear SLIM ion path was implemented that had a "gate" for blocking and accumulating ions for arbitrary time periods. Removing the gate potential caused ions to exit, and the spatial distributions of accumulated ions examined. The ion populations for a set of peptides increased approximately linearly with increased accumulation times until space change effects became significant, after which the peptide precursor ion populations decreased due to growing space charge-related ion activation, reactions, and losses. Ion activation increased with added storage times and the TW amplitude. Lower amplitude TWs in the accumulation/storage region prevented or minimized ion losses or ion heating effects that can also lead to fragmentation. Our results supported the use of an accumulation region close to the SLIM entrance for speeding accumulation, minimizing ion heating, and avoiding ion population profiles that result in IMS peak tailing. Importantly, space charge-driven separations were observed for large populations of accumulated species and attributed to the opposing effects of space charge and the TW. In these separations, ion species form distributions or peaks, sometimes moving against the TW, and are ordered in the SLIM based on their mobilities. Only the highest mobility ions located closest to the gate in the trapped ion population (and where the highest ion densities were achieved) were significantly activated. The observed separations may offer utility for ion prefractionation of ions and increasing the dynamic range measurements, increasing the resolving power of IMS separations by decreasing peak widths for accumulated ion populations, and other purposes benefiting from separations of extremely large ion populations.
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Affiliation(s)
- Pearl Kwantwi-Barima
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Sandilya V. B. Garimella
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Isaac K. Attah
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Xueyun Zheng
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Yehia M. Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
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5
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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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6
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Claes BR, Bowman AP, Poad BLJ, Heeren RMA, Blanksby SJ, Ellis SR. Isomer-Resolved Mass Spectrometry Imaging of Acidic Phospholipids. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2269-2277. [PMID: 37581874 PMCID: PMC10557375 DOI: 10.1021/jasms.3c00192] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/16/2023]
Abstract
The biological functions of lipids are entirely dependent on their molecular structures with even small changes in structure─such as different sites of unsaturation─providing critical markers for changes in the underlying metabolism. Conventional mass spectrometry imaging (MSI) approaches, however, face the twin challenges of mixture and structural complexity and are typically unable to differentiate lipid isomers that differ only in the position(s) of carbon-carbon double bonds. Recent coupling of ozone-induced dissociation (OzID) with matrix-assisted laser desorption/ionization (MALDI)-MSI has demonstrated the potential to map changes in individual double-bond isomers, thus enabling visualization of the modulation in lipid desaturation in adjacent tissue types. This has, to date, only been performed in positive-ion mode due to a generally higher abundance of phosphatidylcholines (PC) in mammalian tissues and the efficient desorption/ionization of this lipid subclass. Many other glycerophospholipids (GPLs), however, are better detected in negative-ion mode as deprotonated anions. Recently, OzID has been implemented on a traveling-wave ion-mobility mass spectrometer (Waters, SYNAPT G2-Si) that provides a 50-fold increase in the rate of the gas-phase reaction between ionized lipids and ozone and a commensurate increase in sensitivity for isomer-resolved mass spectrometry. These gains are exploited here to interrogate the distributions of anionic GPL isomers in biological tissues, covering the subclasses phosphatidylserine (PS), phosphatidylethanolamine (PE), phosphatidylinositol (PI), phosphatidylglycerol (PG), and phosphatidic acid (PA). Exploiting both ozone- and collision-induced dissociation in a single acquisition simultaneously identifies sites of unsaturation and acyl chain composition from the same mass spectrum.
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Affiliation(s)
- Britt
S. R. Claes
- The
Maastricht MultiModal Molecular Imaging (M4I) institute, Division
of Imaging Mass Spectrometry (IMS), Maastricht
University, 6229 ER Maastricht, The Netherlands
| | - Andrew P. Bowman
- The
Maastricht MultiModal Molecular Imaging (M4I) institute, Division
of Imaging Mass Spectrometry (IMS), Maastricht
University, 6229 ER Maastricht, The Netherlands
| | - Berwyck L. J. Poad
- Central
Analytical Research Facility, Queensland
University of Technology, Brisbane, Queensland 4000, Australia
- School
of Chemistry and Physics, Queensland University
of Technology, Brisbane, Queensland 4000, Australia
| | - Ron M. A. Heeren
- The
Maastricht MultiModal Molecular Imaging (M4I) institute, Division
of Imaging Mass Spectrometry (IMS), Maastricht
University, 6229 ER Maastricht, The Netherlands
| | - Stephen J. Blanksby
- Central
Analytical Research Facility, Queensland
University of Technology, Brisbane, Queensland 4000, Australia
- School
of Chemistry and Physics, Queensland University
of Technology, Brisbane, Queensland 4000, Australia
| | - Shane R. Ellis
- The
Maastricht MultiModal Molecular Imaging (M4I) institute, Division
of Imaging Mass Spectrometry (IMS), Maastricht
University, 6229 ER Maastricht, The Netherlands
- Molecular
Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
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7
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He Y, Qin H, Wen J, Cao W, Yan Y, Sun Y, Yuan P, Sun B, Fan S, Lu W, Li C. Characterization of Key Compounds of Organic Acids and Aroma Volatiles in Fruits of Different Actinidia argute Resources Based on High-Performance Liquid Chromatography (HPLC) and Headspace Gas Chromatography-Ion Mobility Spectrometry (HS-GC-IMS). Foods 2023; 12:3615. [PMID: 37835267 PMCID: PMC10572923 DOI: 10.3390/foods12193615] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/22/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
Actinidia arguta, known for its distinctive flavor and high nutritional value, has seen an increase in cultivation and variety identification. However, the characterization of its volatile aroma compounds remains limited. This study aimed to understand the flavor quality and key volatile aroma compounds of different A. arguta fruits. We examined 35 A. arguta resource fruits for soluble sugars, titratable acids, and sugar-acid ratios. Their organic acids and volatile aroma compounds were analyzed using high-performance liquid chromatography (HPLC) and headspace gas chromatography-ion mobility spectrometry (HS-GC-IMS). The study found that among the 35 samples tested, S12 had a higher sugar-acid ratio due to its higher sugar content despite having a high titratable acid content, making its fruit flavor superior to other sources. The A. arguta resource fruits can be classified into two types: those dominated by citric acid and those dominated by quinic acid. The analysis identified a total of 76 volatile aroma substances in 35 A. arguta resource fruits. These included 18 esters, 14 alcohols, 16 ketones, 12 aldehydes, seven terpenes, three pyrazines, two furans, two acids, and two other compounds. Aldehydes had the highest relative content of total volatile compounds. Using the orthogonal partial least squares discriminant method (OPLS-DA) analysis, with the 76 volatile aroma substances as dependent variables and different soft date kiwifruit resources as independent variables, 33 volatile aroma substances with variable importance in projection (VIP) greater than 1 were identified as the main aroma substances of A. arguta resource fruits. The volatile aroma compounds with VIP values greater than 1 were analyzed for odor activity value (OAV). The OAV values of isoamyl acetate, 3-methyl-1-butanol, 1-hexanol, and butanal were significantly higher than those of the other compounds. This suggests that these four volatile compounds contribute more to the overall aroma of A. arguta. This study is significant for understanding the differences between the fruit aromas of different A. arguta resources and for scientifically recognizing the characteristic compounds of the fruit aromas of different A. arguta resources.
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Affiliation(s)
- Yanli He
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.H.); (H.Q.); (J.W.); (W.C.); (Y.Y.); (Y.S.); (P.Y.); (S.F.); (W.L.)
| | - Hongyan Qin
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.H.); (H.Q.); (J.W.); (W.C.); (Y.Y.); (Y.S.); (P.Y.); (S.F.); (W.L.)
| | - Jinli Wen
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.H.); (H.Q.); (J.W.); (W.C.); (Y.Y.); (Y.S.); (P.Y.); (S.F.); (W.L.)
| | - Weiyu Cao
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.H.); (H.Q.); (J.W.); (W.C.); (Y.Y.); (Y.S.); (P.Y.); (S.F.); (W.L.)
| | - Yiping Yan
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.H.); (H.Q.); (J.W.); (W.C.); (Y.Y.); (Y.S.); (P.Y.); (S.F.); (W.L.)
| | - Yining Sun
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.H.); (H.Q.); (J.W.); (W.C.); (Y.Y.); (Y.S.); (P.Y.); (S.F.); (W.L.)
| | - Pengqiang Yuan
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.H.); (H.Q.); (J.W.); (W.C.); (Y.Y.); (Y.S.); (P.Y.); (S.F.); (W.L.)
| | - Bowei Sun
- Faculty of Agriculture, Yanbian University, Yanji 136200, China;
| | - Shutian Fan
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.H.); (H.Q.); (J.W.); (W.C.); (Y.Y.); (Y.S.); (P.Y.); (S.F.); (W.L.)
| | - Wenpeng Lu
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.H.); (H.Q.); (J.W.); (W.C.); (Y.Y.); (Y.S.); (P.Y.); (S.F.); (W.L.)
| | - Changyu Li
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.H.); (H.Q.); (J.W.); (W.C.); (Y.Y.); (Y.S.); (P.Y.); (S.F.); (W.L.)
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8
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Naylor CN, Nagy G. Permethylation and Metal Adduction: A Toolbox for the Improved Characterization of Glycolipids with Cyclic Ion Mobility Separations Coupled to Mass Spectrometry. Anal Chem 2023; 95:13725-13732. [PMID: 37650842 DOI: 10.1021/acs.analchem.3c03448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Lipids are an important class of molecules involved in various biological functions but remain difficult to characterize through mass-spectrometry-based methods because of their many possible isomers. Glycolipids, specifically, play important roles in cell signaling but display an even greater level of isomeric heterogeneity as compared to other lipid classes stemming from the introduction of a carbohydrate and its corresponding linkage position and α/β anomericity at the headgroup. While liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) remains the gold standard technique in lipidomics, it is still unable to characterize all isomeric species, thus presenting the need for new, orthogonal, methodologies. Ion mobility spectrometry-mass spectrometry (IMS-MS) can provide an additional dimension of information that supplements LC-MS/MS workflows, but has seen little use for glycolipid analyses. Herein, we present an analytical toolbox that enables the characterization of various glycolipid isomer sets using high-resolution cyclic ion mobility separations coupled with mass spectrometry (cIMS-MS). Specifically, we utilized a combination of both permethylation and metal adduction to fully resolve isomeric sphingolipids and ceramides with our cIMS-MS platform. We also introduce a new metric that can enable comparing peak-to-peak resolution across varying cIMS-MS pathlengths. Overall, we envision that our presented methodologies are highly amenable to existing LC-MS/MS-based workflows and can also have broad utility toward other omics-based analyses.
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Affiliation(s)
- Cameron N Naylor
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Gabe Nagy
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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9
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Ross DH, Lee JY, Bilbao A, Orton DJ, Eder JG, Burnet MC, Deatherage Kaiser BL, Kyle JE, Zheng X. LipidOz enables automated elucidation of lipid carbon-carbon double bond positions from ozone-induced dissociation mass spectrometry data. Commun Chem 2023; 6:74. [PMID: 37076550 PMCID: PMC10115790 DOI: 10.1038/s42004-023-00867-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/24/2023] [Indexed: 04/21/2023] Open
Abstract
Lipids play essential roles in many biological processes and disease pathology, but unambiguous identification of lipids is complicated by the presence of multiple isomeric species differing by fatty acyl chain length, stereospecifically numbered (sn) position, and position/stereochemistry of double bonds. Conventional liquid chromatography-mass spectrometry (LC-MS/MS) analyses enable the determination of fatty acyl chain lengths (and in some cases sn position) and number of double bonds, but not carbon-carbon double bond positions. Ozone-induced dissociation (OzID) is a gas-phase oxidation reaction that produces characteristic fragments from lipids containing double bonds. OzID can be incorporated into ion mobility spectrometry (IMS)-MS instruments for the structural characterization of lipids, including additional isomer separation and confident assignment of double bond positions. The complexity and repetitive nature of OzID data analysis and lack of software tool support have limited the application of OzID for routine lipidomics studies. Here, we present an open-source Python tool, LipidOz, for the automated determination of lipid double bond positions from OzID-IMS-MS data, which employs a combination of traditional automation and deep learning approaches. Our results demonstrate the ability of LipidOz to robustly assign double bond positions for lipid standard mixtures and complex lipid extracts, enabling practical application of OzID for future lipidomics.
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Affiliation(s)
- Dylan H Ross
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Joon-Yong Lee
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA
- PrognomiQ, Inc, San Mateo, CA, 94403, USA
| | - Aivett Bilbao
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Daniel J Orton
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Josie G Eder
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Meagan C Burnet
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | | | - Jennifer E Kyle
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Xueyun Zheng
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
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10
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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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11
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Przybylski C, Bonnet V. Probing topology of supramolecular complexes between cyclodextrins and alkali metals by ion mobility-mass spectrometry. Carbohydr Polym 2022; 297:120019. [DOI: 10.1016/j.carbpol.2022.120019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/19/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022]
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12
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Cai Y, Zhou Z, Zhu ZJ. Advanced analytical and informatic strategies for metabolite annotation in untargeted metabolomics. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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13
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Gonzalez LE, Szalwinski LJ, Sams TC, Dziekonski ET, Cooks RG. Metabolomic and Lipidomic Profiling of Bacillus Using Two-Dimensional Tandem Mass Spectrometry. Anal Chem 2022; 94:16838-16846. [DOI: 10.1021/acs.analchem.2c03961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- L. Edwin Gonzalez
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Lucas J. Szalwinski
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Thomas C. Sams
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Eric T. Dziekonski
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - R. Graham Cooks
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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14
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Chen X, Tang S, Freitas D, Hirtzel E, Cheng H, Yan X. Characterization of glycerophospholipids at multiple isomer levels via Mn(II)-catalyzed epoxidation. Analyst 2022; 147:4838-4844. [PMID: 36128870 PMCID: PMC9704799 DOI: 10.1039/d2an01174c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Characterization of glycerophospholipid isomers is of significant importance as they play different roles in physiological and pathological processes. In this work, we present a novel and bifunctional derivatization method utilizing Mn(II)-catalyzed epoxidation to simultaneously identify carbon-carbon double bond (CC bond)- and stereonumbering (sn)-positional isomers of phosphatidylcholine. Mn(II) coordinates with picolinic acid and catalyzes epoxidation of unsaturated lipids by peracetic acid. Collision-induced dissociation (CID) of the epoxides generates diagnostic ions that can be used to locate CC bond positions. Meanwhile, CID of Mn(II) ion-lipid complexes produces characteristic ions for determination of sn positions. This bifunctional derivatization takes place in seconds, and the diagnostic ions produced in CID are clear and easy to interpret. Moreover, relative quantification of CC bond-and sn-positional isomers was achieved. The capability of this method in identifying lipids at multiple isomer levels was shown using lipid standards and lipid extracts from complex biological samples.
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Affiliation(s)
- Xi Chen
- Department of Chemistry, Texas A&M University, 580 Ross St, College Station, TX 77843, USA.
| | - Shuli Tang
- Department of Chemistry, Texas A&M University, 580 Ross St, College Station, TX 77843, USA.
| | - Dallas Freitas
- Department of Chemistry, Texas A&M University, 580 Ross St, College Station, TX 77843, USA.
| | - Erin Hirtzel
- Department of Chemistry, Texas A&M University, 580 Ross St, College Station, TX 77843, USA.
| | - Heyong Cheng
- Department of Chemistry, Texas A&M University, 580 Ross St, College Station, TX 77843, USA.
| | - Xin Yan
- Department of Chemistry, Texas A&M University, 580 Ross St, College Station, TX 77843, USA.
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15
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Tang S, Chen X, Ke Y, Wang F, Yan X. Voltage-Controlled Divergent Cascade of Electrochemical Reactions for Characterization of Lipids at Multiple Isomer Levels Using Mass Spectrometry. Anal Chem 2022; 94:12750-12756. [PMID: 36087069 PMCID: PMC10386884 DOI: 10.1021/acs.analchem.2c02375] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cascading divergent reactions in a single system is highly desirable for their intrinsic efficiency and potential to achieve multilevel structural characterization of complex biomolecules. In this work, two electrochemical reactions, interfacial electro-epoxidation and cobalt anodic corrosion, are divergently cascaded in nanoelectrospray (nESI) and can be switched at different voltages. We applied these reactions to lipid identification at multiple isomer levels using mass spectrometry (MS), which remains a great challenge in structural lipidomics. The divergent cascade reactions in situ derivatize lipids to produce epoxidized lipids and cobalt-adducted lipids at different voltages. These lipids are then fragmented upon low-energy collision-induced dissociation (CID), generating diagnostic fragments to indicate C═C locations and sn-positions that cannot be achieved by the low-energy CID of native lipids. We have demonstrated that lipid structural isomers show significantly different profiles in the analysis of healthy and cancerous mouse prostate samples using this strategy. The application of divergent cascade reactions in lipid identification allows the four-in-one analysis of lipid headgroups, fatty acyl chains, C═C locations, and sn-positions simply by tuning the nESI voltages within a single experiment. This feature as well as its low sample consumption, no need for an extra apparatus, and quantitative analysis capability show its great potential in lipidomics.
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Affiliation(s)
- Shuli Tang
- Department of Chemistry, Texas A&M University, 580 Ross Street, College Station, Texas 77843, United States
| | - Xi Chen
- Department of Chemistry, Texas A&M University, 580 Ross Street, College Station, Texas 77843, United States
| | - Yuepeng Ke
- Center for Translational Cancer Research, Texas A&M Institute of Biosciences and Technology, Texas A&M University, Houston, Texas 77030, United States
| | - Fen Wang
- Center for Translational Cancer Research, Texas A&M Institute of Biosciences and Technology, Texas A&M University, Houston, Texas 77030, United States
| | - Xin Yan
- Department of Chemistry, Texas A&M University, 580 Ross Street, College Station, Texas 77843, United States
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16
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Cao W, Shu N, Wen J, Yang Y, Jin Y, Lu W. Characterization of the Key Aroma Volatile Compounds in Nine Different Grape Varieties Wine by Headspace Gas Chromatography-Ion Mobility Spectrometry (HS-GC-IMS), Odor Activity Values (OAV) and Sensory Analysis. Foods 2022; 11:foods11182767. [PMID: 36140895 PMCID: PMC9497463 DOI: 10.3390/foods11182767] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/24/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
During this study, the physicochemical properties, color, and volatile aroma compounds of the original wines produced from the grape varieties ‘Hassan’, ‘Zuoshaner’, ‘Beibinghong’, ‘Zuoyouhong’, ‘Beta’, ‘Shuanghong’, ‘Zijingganlu’, ‘Cabernet Sauvignon’, and ‘Syrah’ were determined and sensory evaluation was performed. Results indicated that ‘Hassan’ contained the most solids, ‘Zuoshaner’ produced the most total acid, residual sugar, total anthocyanin, and total phenol, and ‘Shuanghong’ produced the most tannin. Calculation of the chroma and hue of the wines according to the CIEL*a*b* parameters revealed that the ‘Cabernet Sauvignon’ wines were the brightest of the nine varieties and that the ‘Zuoshaner’ wines had the greatest red hue and yellow hue and the greatest saturation’. A total of 52 volatile compounds were identified and quantified in nine wine samples by HS-GC-IMS analysis, with the most significant number of species detected being 20 esters, followed by 16 alcohols, 8 aldehydes, four ketones, one terpene, and one furan, with the highest total volatile compound content being ‘Beta’. A total of 14 volatile components with OAV (odor activity value) >1 were calculated using the odor activity value (OAV) of the threshold of the aromatic compound, and the OPLS-DA analysis was performed by orthogonal partial least squares discriminant analysis (OPLS-DA) using the OAV values of the compounds with OAV values >1 as the Y variable. The VIP (Variable Importance in Projection) values of six compounds, ethyl isobutyrate, ethyl hexanoate-D, 2-methylpropanal, ethyl octanoate, ethyl butanoate-D, and Isoamyl acetate-D, were calculated to be higher than one between groups, indicating that these six compounds may influence aroma differences. It is essential to recognize that the results of this study have implications for understanding the quality differences between different varieties of wines and for developing wines that have the characteristics of those varieties.
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17
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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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18
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Liu W, Zhang WD, Li T, Zhou Z, Luo M, Chen X, Cai Y, Zhu ZJ. Four-Dimensional Untargeted Profiling of N-Acylethanolamine Lipids in the Mouse Brain Using Ion Mobility–Mass Spectrometry. Anal Chem 2022; 94:12472-12480. [DOI: 10.1021/acs.analchem.2c02650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wenbin Liu
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wei-dong Zhang
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China
| | - Tongzhou Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhiwei Zhou
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Mingdu Luo
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xi Chen
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yuping Cai
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zheng-Jiang Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
- Shanghai Key Laboratory of Aging Studies, 100 Hai Ke Road, Pudong, Shanghai 201210, China
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19
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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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20
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Feng G, Gao M, Wang L, Chen J, Hou M, Wan Q, Lin Y, Xu G, Qi X, Chen S. Dual-resolving of positional and geometric isomers of C=C bonds via bifunctional photocycloaddition-photoisomerization reaction system. Nat Commun 2022; 13:2652. [PMID: 35550511 PMCID: PMC9098869 DOI: 10.1038/s41467-022-30249-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 04/22/2022] [Indexed: 11/11/2022] Open
Abstract
The biological functions of lipids largely depend on their chemical structures. The position and configuration of C=C bonds are two of the essential attributes that determine the structures of unsaturated lipids. However, simultaneous identification of both attributes remains challenging. Here, we develop a bifunctional visible-light-activated photocycloaddition-photoisomerization reaction system, which enables the dual-resolving of the positional and geometric isomerism of C=C bonds in lipids when combines with liquid chromatography-mass spectrometry. The dual-pathway reaction mechanism is demonstrated by experiments and density functional theory calculations. Based on this bifunctional reaction system, a workflow of deep structural lipidomics is established, and allows the revealing of unique patterns of cis-trans-isomers in bacteria, as well as the tracking of C=C positional isomers changes in mouse brain ischemia. This study not only offers a powerful tool for deep lipid structural biology, but also provides a paradigm for developing the multifunctional visible-light-induced reaction. The simultaneous identification of position and configuration of double bonds in unsaturated lipids is challenging. Here, the authors develop a workflow for deep structural lipidomics to address this issue using a bifunctional reaction system combined with liquid chromatography-mass spectrometry, revealing double bond patterns in bacteria and in mouse brain ischemia.
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Affiliation(s)
- Guifang Feng
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei, 430072, China
| | - Ming Gao
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei, 430072, China
| | - Liwei Wang
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei, 430072, China
| | - Jiayi Chen
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Menglu Hou
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei, 430072, China
| | - Qiongqiong Wan
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei, 430072, China
| | - Yun Lin
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Guoyong Xu
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei, 430072, China
| | - Xiaotian Qi
- Engineering Research Center of Organosilicon Compounds & Materials, Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Suming Chen
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei, 430072, China.
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21
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Kwantwi-Barima P, Harrilal CP, Garimella SVB, Attah IK, Smith RD, Ibrahim YM. Effect of Traveling Waveform Profiles on Collision Cross Section Measurements in Structures for Lossless Ion Manipulations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:783-792. [PMID: 35437008 PMCID: PMC10634343 DOI: 10.1021/jasms.1c00364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We evaluated the effect of four different waveform profiles (Square, Sine, Triangle, and asymmetric Sawtooth) on the accuracy of collision cross section (CCS) measurements using traveling wave ion mobility spectrometry (TWIMS) separations in structures for lossless ion manipulations (SLIM). The effects of the waveform profiles on the accuracy of the CCS measurements were evaluated for four classes of compounds (lipids, peptides, steroids, and nucleosides) at different TW speeds (126-206 m/s) and amplitudes (15-89 V). For the lipids and peptides, the TWIMS-based CCS (TWCCS) deviations from the corresponding drift-tube-based CCS (DTCCS) measurements were significantly lower in experiments conducted using the Sawtooth waveform compared to the square waveform. This observation can be rationalized by the lower maximum electric field experienced by ions with a Sawtooth waveform, as compared to the other waveforms, resulting in a lower probability for significant ion heating. We also observed that given approximately comparable resolution for all four waveforms, the Sawtooth waveform resulted in lower TWCCS error and a better agreement with DTCCS values than the Square waveform. In addition, for the steroids and nucleosides, an opposite TWCCS trend was observed, with higher errors with the Sawtooth waveform and lower with the Square waveform, suggesting that these molecules tend to become slightly more compact under ion heating conditions. Under optimum conditions, all TWCCS measurements on the SLIM platform were within 0.5% of those measured in the drift tube ion mobility spectrometry.
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Affiliation(s)
- Pearl Kwantwi-Barima
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Christopher P Harrilal
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Sandilya V B Garimella
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Isaac K Attah
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Yehia M Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
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22
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Li HF, Zhao J, Cao W, Zhang W, Xia Y, Ouyang Z. Site-Specific Photochemical Reaction for Improved C=C Location Analysis of Unsaturated Lipids by Ultraviolet Photodissociation. RESEARCH (WASHINGTON, D.C.) 2022; 2022:9783602. [PMID: 35252873 PMCID: PMC8859641 DOI: 10.34133/2022/9783602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 01/16/2022] [Indexed: 11/16/2022]
Abstract
Unraveling the complexity of the lipidome requires the development of novel approaches to facilitate structural identification and characterization of lipid species with isomer-level discrimination. Ultraviolet photodissociation tandem mass spectrometry (UVPD MS/MS) is a promising tool for structure determination of lipids. The sensitivity of UVPD for lipid analysis however is limited mainly due to weak absorption of UV photons by a C=C. Herein, a C=C site-specific derivatization, the Paternò-Büchi (PB) reaction, was used to incorporate a chromophore to the C=C moiety in fatty acyls, leading to significantly improved UVPD efficiency and sensitivity for pinpointing C=C locations. The wavelength-dependent photodissociation of the PB products demonstrated 4-CF3-benzophenone as the best reagent for UVPD in terms of the efficiency of generating C=C diagnostic fragments and simplicity for C=C location assignments. We demonstrated the effectiveness of this approach for the shotgun profiling of C=C location isomers in different lipid classes from complex lipid extracts, highlighting its potential to advancing the identification of the C=C bond locations in unsaturated lipids.
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Affiliation(s)
- Hai-Fang Li
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Jing Zhao
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Wenbo Cao
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Wenpeng Zhang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Yu Xia
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Zheng Ouyang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
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23
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Hou Y, Gao Y, Guo S, Zhang Z, Chen R, Zhang X. Applications of spatially resolved omics in the field of endocrine tumors. Front Endocrinol (Lausanne) 2022; 13:993081. [PMID: 36704039 PMCID: PMC9873308 DOI: 10.3389/fendo.2022.993081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023] Open
Abstract
Endocrine tumors derive from endocrine cells with high heterogeneity in function, structure and embryology, and are characteristic of a marked diversity and tissue heterogeneity. There are still challenges in analyzing the molecular alternations within the heterogeneous microenvironment for endocrine tumors. Recently, several proteomic, lipidomic and metabolomic platforms have been applied to the analysis of endocrine tumors to explore the cellular and molecular mechanisms of tumor genesis, progression and metastasis. In this review, we provide a comprehensive overview of spatially resolved proteomics, lipidomics and metabolomics guided by mass spectrometry imaging and spatially resolved microproteomics directed by microextraction and tandem mass spectrometry. In this regard, we will discuss different mass spectrometry imaging techniques, including secondary ion mass spectrometry, matrix-assisted laser desorption/ionization and desorption electrospray ionization. Additionally, we will highlight microextraction approaches such as laser capture microdissection and liquid microjunction extraction. With these methods, proteins can be extracted precisely from specific regions of the endocrine tumor. Finally, we compare applications of proteomic, lipidomic and metabolomic platforms in the field of endocrine tumors and outline their potentials in elucidating cellular and molecular processes involved in endocrine tumors.
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Affiliation(s)
- Yinuo Hou
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Yan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Shudi Guo
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Zhibin Zhang
- General Surgery, Tianjin First Center Hospital, Tianjin, China
- *Correspondence: Zhibin Zhang, ; Ruibing Chen, ; Xiangyang Zhang,
| | - Ruibing Chen
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- *Correspondence: Zhibin Zhang, ; Ruibing Chen, ; Xiangyang Zhang,
| | - Xiangyang Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- *Correspondence: Zhibin Zhang, ; Ruibing Chen, ; Xiangyang Zhang,
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24
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Dubland JA. Lipid analysis by ion mobility spectrometry combined with mass spectrometry: A brief update with a perspective on applications in the clinical laboratory. J Mass Spectrom Adv Clin Lab 2022; 23:7-13. [PMID: 34988541 PMCID: PMC8703053 DOI: 10.1016/j.jmsacl.2021.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 11/15/2022] Open
Abstract
Ion mobility spectrometry (IMS) is an analytical technique where ions are separated in the gas phase based on their mobility through a buffer gas in the presence of an electric field. An ion passing through an IMS device has a characteristic collisional cross section (CCS) value that depends on the buffer gas used. IMS can be coupled with mass spectrometry (MS), which characterizes an ion based on a mass-to-charge ratio (m/z), to increase analytical specificity and provide further physicochemical information. In particular, IMS-MS is of ever-increasing interest for the analysis of lipids, which can be problematic to accurately identify and quantify in bodily fluids by liquid chromatography (LC) with MS alone due to the presence of isomers, isobars, and structurally similar analogs. IMS provides an additional layer of separation when combined with front-end LC approaches, thereby, enhancing peak capacity and analytical specificity. CCS (and also ion mobility drift time) can be plotted against m/z ion intensity and/or LC retention time in order to generate in-depth molecular profiles of a sample. Utilization of IMS-MS for routine clinical laboratory testing remains relatively unexplored, but areas do exist for potential implementation. A brief update is provided here on lipid analysis using IMS-MS with a perspective on some applications in the clinical laboratory.
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Key Words
- CCS, collisional cross section
- CV, compensation voltage
- CVD, cardiovascular disease
- Clinical analysis
- DG, diacylglycerol
- DMS, differential mobility spectrometry
- DTIMS, drift tube ion mobility spectrometry
- EV, elution voltage
- FAIMS, field asymmetric waveform ion mobility spectrometry
- FIA, flow injection analysis
- FTICR, fourier-transform ion cyclotron resonance
- HDL, high-density-lipoprotein
- HRMS, high-resolution mass spectrometry
- IMS, ion mobility spectrometry
- IMS-MS, ion mobility spectrometry-mass spectrometry
- Ion mobility spectrometry
- LC, liquid chromatography
- LDL, low-density-lipoprotein
- LPC, lysophosphatidylcholine
- Lipids
- MALDI, matrix-assisted laser desorption/ionization
- MS, mass spectrometry
- Mass spectrometry
- NBS, newborn screening
- PC, glycerophosphocholine
- PE, phosphatidylethanolamine
- PG, phosphatidylglycerol
- RF, radio frequency
- SLIM, structures for loss less ion manipulations
- SM, sphingomyelin
- SV, separation voltage
- TG, triglyceride
- TIMS, trapped ion mobility spectrometry
- TOF, time-of-flight
- TWIMS, traveling wave ion mobility spectrometry
- VLDL, very-low-density lipoprotein
- m/z, mass-to-charge ratio
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Affiliation(s)
- Joshua A. Dubland
- Department of Pathology and Laboratory Medicine, BC Children’s Hospital, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
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25
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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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26
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Jaisinghani N, Seeliger JC. Recent advances in the mass spectrometric profiling of bacterial lipids. Curr Opin Chem Biol 2021; 65:145-153. [PMID: 34600165 DOI: 10.1016/j.cbpa.2021.08.003] [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: 06/21/2021] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 11/19/2022]
Abstract
Exploring the lipids of bacteria presents a predicament that may not be broadly recognized in a field dominated by the biology and biochemistry of eukaryotic - and especially, mammalian - lipids. Bacteria make multifarious metabolites that contain fatty acyl chains of unusual length and unsaturation attached to assorted headgroups, including sugars and fatty alcohols. Lipid profiling approaches developed for eukaryotic lipids often fail to detect, resolve, or identify bacterial lipids due to their wide range of polarities (including very hydrophobic species) and diverse positional and stereochemical variations. Global lipid profiling, or lipidomics, of bacteria has thus developed as a separate mission with methodological and scientific considerations tailored to the biology of these organisms. In this review, we summarize findings primarily from the last three years that exemplify recent advances and continuing challenges to learning about bacterial lipids.
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Affiliation(s)
- Neetika Jaisinghani
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Jessica C Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, 11794, USA.
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27
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Gonzalez LE, Szalwinski LJ, Marsh BM, Wells JM, Cooks RG. Immediate and sensitive detection of sporulated Bacillus subtilis by microwave release and tandem mass spectrometry of dipicolinic acid. Analyst 2021; 146:7104-7108. [PMID: 34757350 DOI: 10.1039/d1an01796a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Spore lysis of Bacillus species is achieved by brief (1 min) microwave irradiation while tandem mass spectrometry (MS/MS) allows identification of the characteristic spore marker, dipicolinic acid. This rapid measurement, made on 105-108 spores, has significant implications for biothreat recognition.
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Affiliation(s)
- L Edwin Gonzalez
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
| | - Lucas J Szalwinski
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
| | - Brett M Marsh
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
| | | | - R Graham Cooks
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
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28
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Xu S, Lv X, Wu B, Xie Y, Wu Z, Tu X, Chen H, Wei F. Pseudotargeted Lipidomics Strategy Enabling Comprehensive Profiling and Precise Lipid Structural Elucidation of Polyunsaturated Lipid-Rich Echium Oil. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:9012-9024. [PMID: 33683118 DOI: 10.1021/acs.jafc.0c07268] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Echium oil has great nutritional value as a result of its high content of α-linolenic acid (ALA, 18:3ω-3) and stearidonic acid (SDA, 18:4ω-3). However, the comprehensive lipid profiling and exact structural characterization of bioactive polyunsaturated lipids in echium oil have not yet been obtained. In this study, we developed a novel pseudotargeted lipidomics strategy for comprehensive profiling and lipid structural elucidation of polyunsaturated lipid-rich echium oil. Our approach integrated untargeted lipidomics analysis with a targeted lipidomics strategy based on Paternò-Büchi (PB)-tandem mass spectrometry (MS/MS) using 2-acetylpyridine (2-AP) as the reaction reagent, allowing for high-coverage lipid profiling and simultaneous determination of C═C locations in triacylglycerols (TGs), diacylglycerols (DGs), free fatty acids (FFAs), and sterol esters (SEs) in echium oil. A total of 209 lipid species were profiled, among which 162 unsaturated lipids were identified with C═C location assignment and 42 groups of ω-3 and ω-6 C═C location isomers were discovered. In addition, relative isomer ratios of certain groups of lipid C═C location isomers were revealed. This pseudotargeted lipidomics strategy described in this study is expected to provide new insight into structural characterization of distinctive bioactive lipids in food.
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Affiliation(s)
- Shuling Xu
- Key Laboratory of Oilseeds Processing of Ministry of Agriculture, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei 430062, People's Republic of China
| | - Xin Lv
- Key Laboratory of Oilseeds Processing of Ministry of Agriculture, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei 430062, People's Republic of China
| | - Bangfu Wu
- Key Laboratory of Oilseeds Processing of Ministry of Agriculture, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei 430062, People's Republic of China
| | - Ya Xie
- Key Laboratory of Oilseeds Processing of Ministry of Agriculture, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei 430062, People's Republic of China
| | - Zongyuan Wu
- Key Laboratory of Oilseeds Processing of Ministry of Agriculture, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei 430062, People's Republic of China
| | - Xinghao Tu
- Key Laboratory of Oilseeds Processing of Ministry of Agriculture, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei 430062, People's Republic of China
| | - Hong Chen
- Key Laboratory of Oilseeds Processing of Ministry of Agriculture, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei 430062, People's Republic of China
| | - Fang Wei
- Key Laboratory of Oilseeds Processing of Ministry of Agriculture, Hubei Key Laboratory of Lipid Chemistry and Nutrition, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, Hubei 430062, People's Republic of China
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29
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Connolly JRFB, Munoz-Muriedas J, Lapthorn C, Higton D, Vissers JPC, Webb A, Beaumont C, Dear GJ. Investigation into Small Molecule Isomeric Glucuronide Metabolite Differentiation Using In Silico and Experimental Collision Cross-Section Values. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1976-1986. [PMID: 34296869 DOI: 10.1021/jasms.0c00427] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Identifying isomeric metabolites remains a challenging and time-consuming process with both sensitivity and unambiguous structural assignment typically only achieved through the combined use of LC-MS and NMR. Ion mobility mass spectrometry (IMMS) has the potential to produce timely and accurate data using a single technique to identify drug metabolites, including isomers, without the requirement for in-depth interpretation (cf. MS/MS data) using an automated computational pipeline by comparison of experimental collision cross-section (CCS) values with predicted CCS values. An ion mobility enabled Q-Tof mass spectrometer was used to determine the CCS values of 28 (14 isomeric pairs of) small molecule glucuronide metabolites, which were then compared to two different in silico models; a quantum mechanics (QM) and a machine learning (ML) approach to test these approaches. The difference between CCS values within isomer pairs was also assessed to evaluate if the difference was large enough for unambiguous structural identification through in silico prediction. A good correlation was found between both the QM- and ML-based models and experimentally determined CCS values. The predicted CCS values were found to be similar between ML and QM in silico methods, with the QM model more accurately describing the difference in CCS values between isomer pairs. Of the 14 isomeric pairs, only one (naringenin glucuronides) gave a sufficient difference in CCS values for the QM model to distinguish between the isomers with some level of confidence, with the ML model unable to confidently distinguish the studied isomer pairs. An evaluation of analyte structures was also undertaken to explore any trends or anomalies within the data set.
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Affiliation(s)
- John R F B Connolly
- RCSI University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin D02 YN77, Ireland
| | | | - Cris Lapthorn
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - David Higton
- Waters Corporation, Stamford Ave, Wilmslow SK9 4AX, United Kingdom
| | | | - Alison Webb
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Claire Beaumont
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Gordon J Dear
- GlaxoSmithKline, Park Road, Ware, Hertfordshire SG12 0DP, United Kingdom
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30
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Fukui S, Sugiyama E, Mizuno H, Sakane I, Asakawa D, Saikusa K, Nishiya Y, Amano Y, Takahara K, Higo D, Toyo'oka T, Todoroki K. Rapid chiral discrimination of oncometabolite dl-2-hydroxyglutaric acid using derivatization and field asymmetric waveform ion mobility spectrometry/mass spectrometry. J Sep Sci 2021; 44:3489-3496. [PMID: 34254740 DOI: 10.1002/jssc.202100350] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/30/2021] [Accepted: 07/11/2021] [Indexed: 01/05/2023]
Abstract
2-Hydroxyglutaric acid is a chiral metabolite whose enantiomers specifically accumulate in different diseases. An enantiomeric excess of the d-form in biological specimens reflects the existence of various pathogenic mutations in cancer patients, however, conventional methods using gas or liquid chromatography and capillary electrophoresis had not been used for large clinical studies because they require multiple analytical instruments and a long run time to separate the enantiomers. Here, we present a rapid separation method for dl-2-hydroxyglutaric acid using a chiral derivatizing reagent and field asymmetric waveform ion mobility spectrometry/mass spectrometry, which requires a single analytical instrument and <1 s for the separation. We compared three derivatization methods and found that a method using (S)-1-(4,6-dimethoxy-1,3,5-triazin-2-yl)pyrrolidin-3-amine enables the separation. In addition, we were able to detect dl-2-hydroxyglutaric acid in standard solution at lower concentrations than that previously reported for the serum. These results show the potential of the method to be used in clinical analysis.
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Affiliation(s)
- Serina Fukui
- Laboratory of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Eiji Sugiyama
- Laboratory of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Hajime Mizuno
- Laboratory of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Iwao Sakane
- ITO EN Ltd., Central Research Institute, Makinohara, Japan
| | - Daiki Asakawa
- National Institute of Advanced Industrial Science and Technology (AIST), National Metrology Institute of Japan (NMIJ), Ibaraki, Japan
| | - Kazumi Saikusa
- National Institute of Advanced Industrial Science and Technology (AIST), National Metrology Institute of Japan (NMIJ), Ibaraki, Japan
| | - Yuki Nishiya
- Laboratory of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yuri Amano
- Laboratory of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | | | | | - Toshimasa Toyo'oka
- Laboratory of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Kenichiro Todoroki
- Laboratory of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
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31
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Zamith-Miranda D, Peres da Silva R, Couvillion SP, Bredeweg EL, Burnet MC, Coelho C, Camacho E, Nimrichter L, Puccia R, Almeida IC, Casadevall A, Rodrigues ML, Alves LR, Nosanchuk JD, Nakayasu ES. Omics Approaches for Understanding Biogenesis, Composition and Functions of Fungal Extracellular Vesicles. Front Genet 2021; 12:648524. [PMID: 34012462 PMCID: PMC8126698 DOI: 10.3389/fgene.2021.648524] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/06/2021] [Indexed: 12/13/2022] Open
Abstract
Extracellular vesicles (EVs) are lipid bilayer structures released by organisms from all kingdoms of life. The diverse biogenesis pathways of EVs result in a wide variety of physical properties and functions across different organisms. Fungal EVs were first described in 2007 and different omics approaches have been fundamental to understand their composition, biogenesis, and function. In this review, we discuss the role of omics in elucidating fungal EVs biology. Transcriptomics, proteomics, metabolomics, and lipidomics have each enabled the molecular characterization of fungal EVs, providing evidence that these structures serve a wide array of functions, ranging from key carriers of cell wall biosynthetic machinery to virulence factors. Omics in combination with genetic approaches have been instrumental in determining both biogenesis and cargo loading into EVs. We also discuss how omics technologies are being employed to elucidate the role of EVs in antifungal resistance, disease biomarkers, and their potential use as vaccines. Finally, we review recent advances in analytical technology and multi-omic integration tools, which will help to address key knowledge gaps in EVs biology and translate basic research information into urgently needed clinical applications such as diagnostics, and immuno- and chemotherapies to fungal infections.
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Affiliation(s)
- Daniel Zamith-Miranda
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States
| | | | - Sneha P. Couvillion
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Erin L. Bredeweg
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Meagan C. Burnet
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Carolina Coelho
- MRC Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
| | - Emma Camacho
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Leonardo Nimrichter
- Laboratório de Glicobiologia de Eucariotos, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rosana Puccia
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina-Universidade Federal de São Paulo, São Paulo, Brazil
| | - Igor C. Almeida
- Department of Biological Sciences, Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX, United States
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Marcio L. Rodrigues
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas-FIOCRUZ PR, Curitiba, Brazil
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lysangela R. Alves
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas-FIOCRUZ PR, Curitiba, Brazil
| | - Joshua D. Nosanchuk
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Ernesto S. Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
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32
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Chen K, Li S, Yang H, Zou J, Yang L, Li J, Ma L. Feasibility of using gas chromatography-ion mobility spectrometry to identify characteristic volatile compounds related to brandy aging. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.103812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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33
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Coupling Machine Learning and Lipidomics as a Tool to Investigate Metabolic Dysfunction-Associated Fatty Liver Disease. A General Overview. Biomolecules 2021; 11:biom11030473. [PMID: 33810079 PMCID: PMC8004861 DOI: 10.3390/biom11030473] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/08/2021] [Accepted: 03/18/2021] [Indexed: 12/15/2022] Open
Abstract
Hepatic biopsy is the gold standard for staging nonalcoholic fatty liver disease (NAFLD). Unfortunately, accessing the liver is invasive, requires a multidisciplinary team and is too expensive to be conducted on large segments of the population. NAFLD starts quietly and can progress until liver damage is irreversible. Given this complex situation, the search for noninvasive alternatives is clinically important. A hallmark of NAFLD progression is the dysregulation in lipid metabolism. In this context, recent advances in the area of machine learning have increased the interest in evaluating whether multi-omics data analysis performed on peripheral blood can enhance human interpretation. In the present review, we show how the use of machine learning can identify sets of lipids as predictive biomarkers of NAFLD progression. This approach could potentially help clinicians to improve the diagnosis accuracy and predict the future risk of the disease. While NAFLD has no effective treatment yet, the key to slowing the progression of the disease may lie in predictive robust biomarkers. Hence, to detect this disease as soon as possible, the use of computational science can help us to make a more accurate and reliable diagnosis. We aimed to provide a general overview for all readers interested in implementing these methods.
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34
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Rivera-Velez SM, Navas J, Villarino NF. Applying metabolomics to veterinary pharmacology and therapeutics. J Vet Pharmacol Ther 2021; 44:855-869. [PMID: 33719079 DOI: 10.1111/jvp.12961] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 02/08/2021] [Indexed: 02/06/2023]
Abstract
Metabolomics is the large-scale study of low-molecular-weight substances in a biological system in a given physiological state at a given time point. Metabolomics can be applied to identify predictors of inter-individual variability in drug response, provide clinicians with data useful for decision-making processes in drug selection, and inform about the pharmacokinetics and pharmacodynamics of a drug. It is, therefore, an exceptional approach for gaining new understanding effects in the field of comparative veterinary pharmacology. However, the incorporation of metabolomics into veterinary pharmacology and toxicology is not yet widespread, and this is probably, at least in part, a result of its highly multidisciplinary nature. This article reviews the potential applications of metabolomics in veterinary pharmacology and therapeutics. It integrates key concepts for designing metabolomics studies and analyzing and interpreting metabolomics data, providing solid foundations for applying metabolomics to the study of drugs in all veterinary species.
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Affiliation(s)
- Sol M Rivera-Velez
- Molecular Determinants Core, Johns Hopkins All Children's Hospital, Saint Petersburg, Florida, USA
| | - Jinna Navas
- Program in Individualized Medicine, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Nicolas F Villarino
- Program in Individualized Medicine, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
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35
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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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36
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Conant CR, Attah IK, Garimella SVB, Nagy G, Bilbao A, Smith RD, Ibrahim YM. Evaluation of Waveform Profiles for Traveling Wave Ion Mobility Separations in Structures for Lossless Ion Manipulations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:225-236. [PMID: 33126794 PMCID: PMC8170696 DOI: 10.1021/jasms.0c00282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Structures for lossless ion manipulations (SLIM) have recently enabled a powerful implementation of traveling wave ion mobility spectrometry (TWIMS) for ultrahigh resolution separations; however, experimental parameters have not been optimized, and potential significant gains may be feasible. Most TWIMS separations have utilized square-shaped waveforms applied by time-dependent voltage stepping across repeating sets of electrodes, but alternative waveforms may provide further improvements to resolution. Here, we characterize five waveforms (including square and sine) in terms of their transmission efficiency, IMS resolution, and resolving power, and explore the effects of TW amplitude and speed on the performance of each. We found, consistent with previous work, separations were generally improved with higher TW amplitudes, moderately improved by lower speeds (limited by ion "surfing" with the waves), and found decreases in signal intensity at the extremes of operating conditions. The triangle and asymmetric "ramp forward" shaped profiles were found to provide modestly greater resolution and resolving power, an observation we tentatively attribute to their relatively uniform fields and minimal low-field regions.
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Affiliation(s)
- Christopher R Conant
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Isaac K Attah
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Sandilya V B Garimella
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Gabe Nagy
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Aivett Bilbao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Yehia M Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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37
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Su Z, Liu B, Ma C. Analyses of the volatile compounds in cherry wine during fermentation and aging in bottle using HS-GC-IMS. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2021. [DOI: 10.3136/fstr.27.599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Zhengbo Su
- Shandong Provincial Key Laboratory of Food and Fermentation Engineering, Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology (Shandong Academy of Sciences)
| | - Baoxiang Liu
- Shandong Provincial Key Laboratory of Food and Fermentation Engineering, Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology (Shandong Academy of Sciences)
| | - Chuang Ma
- Shandong Provincial Key Laboratory of Food and Fermentation Engineering, Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology (Shandong Academy of Sciences)
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38
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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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39
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Alves MA, Lamichhane S, Dickens A, McGlinchey A, Ribeiro HC, Sen P, Wei F, Hyötyläinen T, Orešič M. Systems biology approaches to study lipidomes in health and disease. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1866:158857. [PMID: 33278596 DOI: 10.1016/j.bbalip.2020.158857] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/13/2020] [Accepted: 11/27/2020] [Indexed: 12/15/2022]
Abstract
Lipids have many important biological roles, such as energy storage sources, structural components of plasma membranes and as intermediates in metabolic and signaling pathways. Lipid metabolism is under tight homeostatic control, exhibiting spatial and dynamic complexity at multiple levels. Consequently, lipid-related disturbances play important roles in the pathogenesis of most of the common diseases. Lipidomics, defined as the study of lipidomes in biological systems, has emerged as a rapidly-growing field. Due to the chemical and functional diversity of lipids, the application of a systems biology approach is essential if one is to address lipid functionality at different physiological levels. In parallel with analytical advances to measure lipids in biological matrices, the field of computational lipidomics has been rapidly advancing, enabling modeling of lipidomes in their pathway, spatial and dynamic contexts. This review focuses on recent progress in systems biology approaches to study lipids in health and disease, with specific emphasis on methodological advances and biomedical applications.
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Affiliation(s)
- Marina Amaral Alves
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Santosh Lamichhane
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Alex Dickens
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Aidan McGlinchey
- School of Medical Sciences, Örebro University, 702 81 Örebro, Sweden
| | | | - Partho Sen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; School of Medical Sciences, Örebro University, 702 81 Örebro, Sweden
| | - Fang Wei
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, PR China
| | | | - Matej Orešič
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; School of Medical Sciences, Örebro University, 702 81 Örebro, Sweden.
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40
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Odenkirk MT, Zin PPK, Ash JR, Reif DM, Fourches D, Baker ES. Structural-based connectivity and omic phenotype evaluations (SCOPE): a cheminformatics toolbox for investigating lipidomic changes in complex systems. Analyst 2020; 145:7197-7209. [PMID: 33094747 PMCID: PMC7695036 DOI: 10.1039/d0an01638a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Since its inception, the main goal of the lipidomics field has been to characterize lipid species and their respective biological roles. However, difficulties in both full speciation and biological interpretation have rendered these objectives extremely challenging and as a result, limited our understanding of lipid mechanisms and dysregulation. While mass spectrometry-based advancements have significantly increased the ability to identify lipid species, less progress has been made surrounding biological interpretations. We have therefore developed a Structural-based Connectivity and Omic Phenotype Evaluations (SCOPE) cheminformatics toolbox to aid in these evaluations. SCOPE enables the assessment and visualization of two main lipidomic associations: structure/biological connections and metadata linkages either separately or in tandem. To assess structure and biological relationships, SCOPE utilizes key lipid structural moieties such as head group and fatty acyl composition and links them to their respective biological relationships through hierarchical clustering and grouped heatmaps. Metadata arising from phenotypic and environmental factors such as age and diet is then correlated with the lipid structures and/or biological relationships, utilizing Toxicological Prioritization Index (ToxPi) software. Here, SCOPE is demonstrated for various applications from environmental studies to clinical assessments to showcase new biological connections not previously observed with other techniques.
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Affiliation(s)
- Melanie T Odenkirk
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA.
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41
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Chen X, Yin Y, Zhou Z, Li T, Zhu ZJ. Development of a combined strategy for accurate lipid structural identification and quantification in ion-mobility mass spectrometry based untargeted lipidomics. Anal Chim Acta 2020; 1136:115-124. [DOI: 10.1016/j.aca.2020.08.048] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/13/2020] [Accepted: 08/24/2020] [Indexed: 10/23/2022]
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42
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Zhang Q, Ding Y, Gu S, Zhu S, Zhou X, Ding Y. Identification of changes in volatile compounds in dry-cured fish during storage using HS-GC-IMS. Food Res Int 2020; 137:109339. [DOI: 10.1016/j.foodres.2020.109339] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/02/2020] [Accepted: 05/17/2020] [Indexed: 01/07/2023]
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43
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Djambazova KV, Klein DR, Migas LG, Neumann EK, Rivera ES, Van de Plas R, Caprioli RM, Spraggins JM. Resolving the Complexity of Spatial Lipidomics Using MALDI TIMS Imaging Mass Spectrometry. Anal Chem 2020; 92:13290-13297. [PMID: 32808523 DOI: 10.1021/acs.analchem.0c02520] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lipids are a structurally diverse class of molecules with important biological functions including cellular signaling and energy storage. Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) allows for direct mapping of biomolecules in tissues. Fully characterizing the structural diversity of lipids remains a challenge due to the presence of isobaric and isomeric species, which greatly complicates data interpretation when only m/z information is available. Integrating ion mobility separations aids in deconvoluting these complex mixtures and addressing the challenges of lipid IMS. Here, we demonstrate that a MALDI quadrupole time-of-flight (Q-TOF) mass spectrometer with trapped ion mobility spectrometry (TIMS) enables a >250% increase in the peak capacity during IMS experiments. MALDI TIMS-MS separation of lipid isomer standards, including sn backbone isomers, acyl chain isomers, and double-bond position and stereoisomers, is demonstrated. As a proof of concept, in situ separation and imaging of lipid isomers with distinct spatial distributions were performed using tissue sections from a whole-body mouse pup.
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Affiliation(s)
- Katerina V Djambazova
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States.,Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Dustin R Klein
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Lukasz G Migas
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Elizabeth K Neumann
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Emilio S Rivera
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Raf Van de Plas
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Richard M Caprioli
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States.,Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States.,Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, Tennessee 37232, United States.,Department of Medicine, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Jeffrey M Spraggins
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States.,Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
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44
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Recent applications of mass spectrometry in bacterial lipidomics. Anal Bioanal Chem 2020; 412:5935-5943. [DOI: 10.1007/s00216-020-02541-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/14/2020] [Accepted: 02/21/2020] [Indexed: 12/11/2022]
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45
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Wu Q, Wang JY, Han DQ, Yao ZP. Recent advances in differentiation of isomers by ion mobility mass spectrometry. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115801] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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46
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Chen X, Zhou Z, Zhu ZJ. The Use of LipidIMMS Analyzer for Lipid Identification in Ion Mobility-Mass Spectrometry-Based Untargeted Lipidomics. Methods Mol Biol 2020; 2084:269-282. [PMID: 31729667 DOI: 10.1007/978-1-0716-0030-6_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Untargeted lipidomics aims to comprehensively measure and characterize all lipid species in biological systems. Ion mobility-mass spectrometry (IM-MS) has showed a great potential for untargeted lipidomic analysis. Coupling with liquid chromatography and data-independent tandem MS techniques, acquired IM-MS data set contains four-dimensional information for lipid identification, including m/z of MS1 ion, retention time (RT), collision cross section (CCS), and MS/MS spectra. In this protocol, we introduced a data processing workflow using an integrative web server, namely, LipidIMMS Analyzer, to support accurate lipid identification. The protocol demonstrated the integration of all four dimensional information to achieve unambiguous identifications of lipids in complex biological samples.
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Affiliation(s)
- Xi Chen
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhiwei Zhou
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zheng-Jiang Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.
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47
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Claes BSR, Takeo E, Fukusaki E, Shimma S, Heeren RMA. Imaging Isomers on a Biological Surface: A Review. Mass Spectrom (Tokyo) 2019; 8:A0078. [PMID: 32158629 PMCID: PMC7035452 DOI: 10.5702/massspectrometry.a0078] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 10/31/2019] [Indexed: 12/30/2022] Open
Abstract
Mass spectrometry imaging is an imaging technology that allows the localization and identification of molecules on (biological) sample surfaces. Obtaining the localization of a compound in tissue is of great value in biological research. Yet, the identification of compounds remains a challenge. Mass spectrometry alone, even with high-mass resolution, cannot always distinguish between the subtle structural differences of isomeric compounds. This review discusses recent advances in mass spectrometry imaging of lipids, steroid hormones, amino acids and proteins that allow imaging with isomeric resolution. These improvements in detailed identification can give new insights into the local biological activity of isomers.
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Affiliation(s)
- Britt S. R. Claes
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University
| | - Emi Takeo
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | - Shuichi Shimma
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | - Ron M. A. Heeren
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University
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48
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Wang J, Han X. Analytical challenges of shotgun lipidomics at different resolution of measurements. Trends Analyt Chem 2019; 121:115697. [PMID: 32713986 PMCID: PMC7382544 DOI: 10.1016/j.trac.2019.115697] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The essence of shotgun lipidomics is to maintain consistency of the chemical environment of lipid samples during mass spectrometry acquisition. This strategy is suitable for large-scale quantitative analysis. This strategy also allows sufficient time to collect data to improve the signal-to-noise ratio. The initial approach of shotgun lipidomics was the electrospray ionization (ESI)-based direct infusion mass spectrometry strategy. With development of mass spectrometry for small molecules, shotgun lipidomics methods have been extended to matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) and ambient mass spectrometry, including MS imaging methods. Furthermore, the object of analysis has extended from organ and body fluid levels to tissue and cell levels with technological developments. In this article, we summarize the status and technical challenges of shotgun lipidomics at different resolution of measurements from the mass spectrometry perspective.
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Affiliation(s)
- Jianing Wang
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 USA
| | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 USA
- Department of Medicine – Diabetes, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 USA
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49
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Zhou Z, Shen X, Chen X, Tu J, Xiong X, Zhu ZJ. LipidIMMS Analyzer: integrating multi-dimensional information to support lipid identification in ion mobility-mass spectrometry based lipidomics. Bioinformatics 2019; 35:698-700. [PMID: 30052780 DOI: 10.1093/bioinformatics/bty661] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/02/2018] [Accepted: 07/20/2018] [Indexed: 12/21/2022] Open
Abstract
SUMMARY Ion mobility-mass spectrometry (IM-MS) has showed great application potential for lipidomics. However, IM-MS based lipidomics is significantly restricted by the available software for lipid structural identification. Here, we developed a software tool, namely, LipidIMMS Analyzer, to support the accurate identification of lipids in IM-MS. For the first time, the software incorporates a large-scale database covering over 260 000 lipids and four-dimensional structural information for each lipid [i.e. m/z, retention time (RT), collision cross-section (CCS) and MS/MS spectra]. Therefore, multi-dimensional information can be readily integrated to support lipid identifications, and significantly improve the coverage and confidence of identification. Currently, the software supports different IM-MS instruments and data acquisition approaches. AVAILABILITY AND IMPLEMENTATION The software is freely available at: http://imms.zhulab.cn/LipidIMMS/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zhiwei Zhou
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaotao Shen
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xi Chen
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jia Tu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xin Xiong
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Zheng-Jiang Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
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50
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Lee TH, Hofferek V, Separovic F, Reid GE, Aguilar MI. The role of bacterial lipid diversity and membrane properties in modulating antimicrobial peptide activity and drug resistance. Curr Opin Chem Biol 2019; 52:85-92. [DOI: 10.1016/j.cbpa.2019.05.025] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/13/2019] [Accepted: 05/27/2019] [Indexed: 12/17/2022]
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