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Singh A, Del Poeta M. Sphingolipidomics: An Important Mechanistic Tool for Studying Fungal Pathogens. Front Microbiol 2016; 7:501. [PMID: 27148190 PMCID: PMC4830811 DOI: 10.3389/fmicb.2016.00501] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 03/28/2016] [Indexed: 01/28/2023] Open
Abstract
Sphingolipids form of a unique and complex group of bioactive lipids in fungi. Structurally, sphingolipids of fungi are quite diverse with unique differences in the sphingoid backbone, amide linked fatty acyl chain and the polar head group. Two of the most studied and conserved sphingolipid classes in fungi are the glucosyl- or galactosyl-ceramides and the phosphorylinositol containing phytoceramides. Comprehensive structural characterization and quantification of these lipids is largely based on advanced analytical mass spectrometry based lipidomic methods. While separation of complex lipid mixtures is achieved through high performance liquid chromatography, the soft - electrospray ionization tandem mass spectrometry allows a high sensitivity and selectivity of detection. Herein, we present an overview of lipid extraction, chromatographic separation and mass spectrometry employed in qualitative and quantitative sphingolipidomics in fungi.
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Affiliation(s)
- Ashutosh Singh
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony BrookNY, USA; Veterans Administration Medical Center, NorthportNY, USA
| | - Maurizio Del Poeta
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony BrookNY, USA; Veterans Administration Medical Center, NorthportNY, USA
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Panchal S, Asati A, Satyanarayana GNV, Raghav A, Ahmad J, Patel DK. Ionic liquid based microextraction of targeted lipids from serum using UPLC-MS/MS with a chemometric approach: a pilot study. RSC Adv 2016. [DOI: 10.1039/c6ra17408f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An ionic liquid based vortex assisted surfactant-enhanced emulsification microextraction method followed by using liquid chromatography-electrospray mass spectrometry have been used for the determination of fatty acids, triglycerides and phospholipids in serum samples.
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Affiliation(s)
- Smita Panchal
- Academy of Scientific & Innovative Research (AcSIR)
- CSIR-IITR Campus
- Lucknow
- India
- Analytical Chemistry Laboratory
| | - Ankita Asati
- Academy of Scientific & Innovative Research (AcSIR)
- CSIR-IITR Campus
- Lucknow
- India
- Analytical Chemistry Laboratory
| | - G. N. V. Satyanarayana
- Analytical Chemistry Laboratory
- Regulatory Toxicology Group
- CSIR-Indian Institute of Toxicology Research
- Lucknow-226001
- India
| | - Alok Raghav
- Rajiv Gandhi Centre for Diabetes & Endocrinology
- Faculty of Medicine
- J. N. Medical College
- Aligarh Muslim University
- Aligarh
| | - Jamal Ahmad
- Rajiv Gandhi Centre for Diabetes & Endocrinology
- Faculty of Medicine
- J. N. Medical College
- Aligarh Muslim University
- Aligarh
| | - Devendra K. Patel
- Academy of Scientific & Innovative Research (AcSIR)
- CSIR-IITR Campus
- Lucknow
- India
- Analytical Chemistry Laboratory
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103
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Oni-Orisan A, Edin ML, Lee JA, Wells MA, Christensen ES, Vendrov KC, Lih FB, Tomer KB, Bai X, Taylor JM, Stouffer GA, Zeldin DC, Lee CR. Cytochrome P450-derived epoxyeicosatrienoic acids and coronary artery disease in humans: a targeted metabolomics study. J Lipid Res 2015; 57:109-19. [PMID: 26555503 DOI: 10.1194/jlr.m061697] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Indexed: 12/15/2022] Open
Abstract
Cytochrome P450 (CYP)-derived epoxyeicosatrienoic acids (EETs) exhibit potent cardiovascular protective effects in preclinical models, and promoting the effects of EETs has emerged as a potential therapeutic strategy for coronary artery disease (CAD). The relationship between circulating EET levels and CAD extent in humans, however, remains unknown. A panel of free (unesterified) plasma eicosanoid metabolites was quantified in 162 patients referred for coronary angiography, and associations with extent of CAD [no apparent CAD (N = 39), nonobstructive CAD (N = 51), and obstructive CAD (N = 72)] were evaluated. A significant relationship between free EET levels and CAD extent was observed (P = 0.003) such that the presence of obstructive CAD was associated with lower circulating EET levels. This relationship was confirmed in multiple regression analysis where CAD extent was inversely and significantly associated with EET levels (P = 0.013), and with a biomarker of EET biosynthesis (P < 0.001), independent of clinical and demographic factors. Furthermore, quantitative enrichment analysis revealed that these associations were the most pronounced compared with other eicosanoid metabolism pathways. Collectively, these findings suggest that the presence of obstructive CAD is associated with lower EET metabolite levels secondary to suppressed EET biosynthesis. Novel strategies that promote the effects of EETs may have therapeutic promise for patients with obstructive CAD.
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Affiliation(s)
- Akinyemi Oni-Orisan
- Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel Hill Eshelman School of Pharmacy, University of North Carolina at Chapel Hill School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC Center for Pharmacogenomics and Individualized Therapy, University of North Carolina at Chapel Hill School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Matthew L Edin
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC
| | - John Andrew Lee
- Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel Hill Eshelman School of Pharmacy, University of North Carolina at Chapel Hill School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Michael A Wells
- Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel Hill Eshelman School of Pharmacy, University of North Carolina at Chapel Hill School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Erin S Christensen
- Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel Hill Eshelman School of Pharmacy, University of North Carolina at Chapel Hill School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kimberly C Vendrov
- Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel Hill Eshelman School of Pharmacy, University of North Carolina at Chapel Hill School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Fred B Lih
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC
| | - Kenneth B Tomer
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC
| | - Xue Bai
- Department of Pathology and Lab Medicine, University of North Carolina at Chapel Hill School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Joan M Taylor
- Department of Pathology and Lab Medicine, University of North Carolina at Chapel Hill School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC McAllister Heart Institute, University of North Carolina at Chapel Hill School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - George A Stouffer
- McAllister Heart Institute, University of North Carolina at Chapel Hill School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC Division of Cardiology, University of North Carolina at Chapel Hill School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Darryl C Zeldin
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC
| | - Craig R Lee
- Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel Hill Eshelman School of Pharmacy, University of North Carolina at Chapel Hill School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC Center for Pharmacogenomics and Individualized Therapy, University of North Carolina at Chapel Hill School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC McAllister Heart Institute, University of North Carolina at Chapel Hill School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
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Tarazona P, Feussner K, Feussner I. An enhanced plant lipidomics method based on multiplexed liquid chromatography-mass spectrometry reveals additional insights into cold- and drought-induced membrane remodeling. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:621-33. [PMID: 26340975 DOI: 10.1111/tpj.13013] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 08/17/2015] [Accepted: 08/26/2015] [Indexed: 05/20/2023]
Abstract
Within the lipidome of plants a few bulk molecular species hamper the detection of the rest, which are present at relatively low levels. In addition, low-abundance species are often masked by numerous isobaric interferences, such as those caused by isoelemental species and isotopologues. This scenario not only means that minor species are underrepresented, but also leads to potential misidentifications and limits the structural information gathered by lipidomics approaches. In order to overcome these limitations we have developed a multiplexed liquid chromatography-mass spectrometry lipidomics platform able to achieve an enhanced coverage of plant lipidomes. The platform is based on a single extraction step followed by a series of ultra-performance liquid chromatography separations. Post-column flow is then directed to both a triple quadrupole analyzer for targeted profiling and a time-of-flight analyzer for accurate mass analysis. As a proof of concept, plants were subjected to cold or drought, which are known to trigger widespread remodeling events in plant cell membranes. Analysis of the leaf lipidome yielded 393 molecular species within 23 different lipid classes. This enhanced coverage allowed us to identify lipid molecular species and even classes that are altered upon stress, allowing hypotheses on role of glycosylinositolphosphoceramides (GIPC), steryl glycosides (SG) and acylated steryl glycosides (ASG) in drought stress to be addressed and confirming the findings from numerous previous studies with a single, wide-ranging lipidomics approach. This extended our knowledge on membrane remodeling during the drought response, integrating sphingolipids and sterol lipids into the current glycerolipid-based model.
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Affiliation(s)
- Pablo Tarazona
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Kirstin Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
- Department of Plant Biochemistry, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
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106
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Zhao Y, Wang M, Lindström ME, Li J. Fatty Acid and Lipid Profiles with Emphasis on n-3 Fatty Acids and Phospholipids from Ciona intestinalis. Lipids 2015; 50:1009-27. [PMID: 26233815 DOI: 10.1007/s11745-015-4049-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 06/23/2015] [Indexed: 11/24/2022]
Abstract
In order to establish Ciona intestinalis as a new bioresource for n-3 fatty acids-rich marine lipids, the animal was fractionated into tunic and inner body tissues prior to lipid extraction. The lipids obtained were further classified into neutral lipids (NL), glycolipids (GL) and phospholipids (PL) followed by qualitative and quantitative analysis using GC-FID, GC-MS, (1)H NMR, 2D NMR, MALDI-TOF-MS and LC-ESI-MS methods. It was found that the tunic and inner body tissues contained 3.42-4.08% and 15.9-23.4% of lipids respectively. PL was the dominant lipid class (42-60%) irrespective of the anatomic fractions. From all lipid fractions and classes, the major fatty acids were 16:0, 18:1n-9, C20:1n-9, C20:5n-3 (EPA) and C22:6n-3 (DHA). The highest amounts of long chain n-3 fatty acids, mainly EPA and DHA, were located in PL from both body fractions. Cholestanol and cholesterol were the dominant sterols together with noticeable amounts of stellasterol, 22 (Z)-dehydrocholesterol and lathosterol. Several other identified and two yet unidentified sterols were observed for the first time from C. intestinalis. Different molecular species of phosphatidylcholine (34 species), sphingomyelin (2 species), phosphatidylethanolamine (2 species), phosphatidylserine (10 species), phosphatidylglycerol (9 species), ceramide (38 species) and lysophospholipid (5 species) were identified, representing the most systematic PL profiling knowledge so far for the animal. It could be concluded that C. intestinalis lipids should be a good alternative for fish oil with high contents of n-3 fatty acids. The lipids would be more bioavailable due to the presence of the fatty acids being mainly in the form of PL.
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Affiliation(s)
- Yadong Zhao
- Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Teknikringen 56-58, 100 44, Stockholm, Sweden
| | - Miao Wang
- Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Teknikringen 56-58, 100 44, Stockholm, Sweden
| | - Mikael E Lindström
- Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Teknikringen 56-58, 100 44, Stockholm, Sweden
| | - Jiebing Li
- Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Teknikringen 56-58, 100 44, Stockholm, Sweden.
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107
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Vergara D, D'Alessandro M, Rizzello A, De Riccardis L, Lunetti P, Del Boccio P, De Robertis F, Trianni G, Maffia M, Giudetti AM. A lipidomic approach to the study of human CD4(+) T lymphocytes in multiple sclerosis. BMC Neurosci 2015. [PMID: 26205308 PMCID: PMC4513631 DOI: 10.1186/s12868-015-0183-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Background Lipids play different important roles in central nervous system so that dysregulation of lipid pathways has been implicated in a growing
number of neurodegenerative disorders including multiple sclerosis (MS). MS is the most prevalent autoimmune disorder of the central nervous system, with neurological symptoms caused by inflammation and demyelination. In this study, a lipidomic analysis was performed for the rapid profile of CD4+ T lymphocytes from MS patient and control samples in an untargeted approach. Methods A matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry based approach was used for the analysis of lipid extracts using 9-aminoacridine as matrix. Lipids were analyzed in negative mode and selected species fragmented using MALDI tandem mass spectrometry for their structural assignments. Results The analysis reveals some modifications in the phospholipid pattern of MS CD4+ T lymphocytes with respect to healthy controls with a significant increase of cardiolipin species in MS samples. Conclusions These results demonstrate the feasibility of a MALDI-TOF approach for the analysis of CD4+ lipid extracts and suggest how alterations in the lipid metabolism characterized lymphocytes of MS patients.
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Affiliation(s)
- Daniele Vergara
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Monteroni, Lecce, Italy. .,Laboratory of Clinical Proteomic, "Giovanni Paolo II" Hospital, ASL-Lecce, Piazzetta F. Muratore, Lecce, Italy.
| | - Michele D'Alessandro
- Department of Medical, Oral and Biotechnological Sciences, Research Centre on Aging (Ce.S.I), "G. d'Annunzio" University Foundation, Chieti-Pescara, Italy.
| | - Antonia Rizzello
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Monteroni, Lecce, Italy. .,Laboratory of Clinical Proteomic, "Giovanni Paolo II" Hospital, ASL-Lecce, Piazzetta F. Muratore, Lecce, Italy.
| | - Lidia De Riccardis
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Monteroni, Lecce, Italy.
| | - Paola Lunetti
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Monteroni, Lecce, Italy.
| | - Piero Del Boccio
- Department of Medical, Oral and Biotechnological Sciences, Research Centre on Aging (Ce.S.I), "G. d'Annunzio" University Foundation, Chieti-Pescara, Italy.
| | - Francesca De Robertis
- Department of Neurology, "Vito Fazzi" Hospital, ASL-Lecce, Piazzetta F. Muratore, Lecce, Italy.
| | - Giorgio Trianni
- Department of Neurology, "Vito Fazzi" Hospital, ASL-Lecce, Piazzetta F. Muratore, Lecce, Italy.
| | - Michele Maffia
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Monteroni, Lecce, Italy. .,Laboratory of Clinical Proteomic, "Giovanni Paolo II" Hospital, ASL-Lecce, Piazzetta F. Muratore, Lecce, Italy.
| | - Anna M Giudetti
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Monteroni, Lecce, Italy.
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Johnson AL, Edson KZ, Totah RA, Rettie AE. Cytochrome P450 ω-Hydroxylases in Inflammation and Cancer. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2015; 74:223-62. [PMID: 26233909 DOI: 10.1016/bs.apha.2015.05.002] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cytochrome P450-dependent ω-hydroxylation is a prototypic metabolic reaction of CYP4 family members that is important for the elimination and bioactivation of not only therapeutic drugs, but also endogenous compounds, principally fatty acids. Eicosanoids, derived from arachidonic acid, are key substrates in the latter category. Human CYP4 enzymes, mainly CYP4A11, CYP4F2, and CYP4F3B, hydroxylate arachidonic acid at the omega position to form 20-HETE, which has important effects in tumor progression and on angiogenesis and blood pressure regulation in the vasculature and kidney. CYP4F3A in myeloid tissue catalyzes the ω-hydroxylation of leukotriene B4 to 20-hydroxy leukotriene B4, an inactivation process that is critical for the regulation of the inflammatory response. Here, we review the enzymology, tissue distribution, and substrate selectivity of human CYP4 ω-hydroxylases and their roles as catalysts for the formation and termination of the biological effects of key eicosanoid metabolites in inflammation and cancer progression.
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Affiliation(s)
- Amanda L Johnson
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, Washington, USA
| | - Katheryne Z Edson
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, Washington, USA; Amgen Inc., Thousand Oaks, California, USA
| | - Rheem A Totah
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, Washington, USA
| | - Allan E Rettie
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, Washington, USA.
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Spickett CM, Pitt AR. Oxidative lipidomics coming of age: advances in analysis of oxidized phospholipids in physiology and pathology. Antioxid Redox Signal 2015; 22:1646-66. [PMID: 25694038 PMCID: PMC4486145 DOI: 10.1089/ars.2014.6098] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
SIGNIFICANCE Oxidized phospholipids are now well recognized as markers of biological oxidative stress and bioactive molecules with both pro-inflammatory and anti-inflammatory effects. While analytical methods continue to be developed for studies of generic lipid oxidation, mass spectrometry (MS) has underpinned the advances in knowledge of specific oxidized phospholipids by allowing their identification and characterization, and it is responsible for the expansion of oxidative lipidomics. RECENT ADVANCES Studies of oxidized phospholipids in biological samples, from both animal models and clinical samples, have been facilitated by the recent improvements in MS, especially targeted routines that depend on the fragmentation pattern of the parent molecular ion and improved resolution and mass accuracy. MS can be used to identify selectively individual compounds or groups of compounds with common features, which greatly improves the sensitivity and specificity of detection. Application of these methods has enabled important advances in understanding the mechanisms of inflammatory diseases such as atherosclerosis, steatohepatitis, leprosy, and cystic fibrosis, and it offers potential for developing biomarkers of molecular aspects of the diseases. CRITICAL ISSUES AND FUTURE DIRECTIONS The future in this field will depend on development of improved MS technologies, such as ion mobility, novel enrichment methods and databases, and software for data analysis, owing to the very large amount of data generated in these experiments. Imaging of oxidized phospholipids in tissue MS is an additional exciting direction emerging that can be expected to advance understanding of physiology and disease.
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Affiliation(s)
- Corinne M. Spickett
- School of Life & Health Sciences, Aston University, Birmingham, United Kingdom
| | - Andrew R. Pitt
- School of Life & Health Sciences, Aston University, Birmingham, United Kingdom
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Sala P, Pötz S, Brunner M, Trötzmüller M, Fauland A, Triebl A, Hartler J, Lankmayr E, Köfeler HC. Determination of oxidized phosphatidylcholines by hydrophilic interaction liquid chromatography coupled to Fourier transform mass spectrometry. Int J Mol Sci 2015; 16:8351-63. [PMID: 25874761 PMCID: PMC4425085 DOI: 10.3390/ijms16048351] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 04/02/2015] [Accepted: 04/08/2015] [Indexed: 01/08/2023] Open
Abstract
A novel liquid chromatography-mass spectrometry (LC-MS) approach for analysis of oxidized phosphatidylcholines by an Orbitrap Fourier Transform mass spectrometer in positive electrospray ionization (ESI) coupled to hydrophilic interaction liquid chromatography (HILIC) was developed. This method depends on three selectivity criteria for separation and identification: retention time, exact mass at a resolution of 100,000 and collision induced dissociation (CID) fragment spectra in a linear ion trap. The process of chromatography development showed the best separation properties with a silica-based Kinetex column. This type of chromatography was able to separate all major lipid classes expected in mammalian samples, yielding increased sensitivity of oxidized phosphatidylcholines over reversed phase chromatography. Identification of molecular species was achieved by exact mass on intact molecular ions and CID tandem mass spectra containing characteristic fragments. Due to a lack of commercially available standards, method development was performed with copper induced oxidation products of palmitoyl-arachidonoyl-phosphatidylcholine, which resulted in a plethora of lipid species oxidized at the arachidonoyl moiety. Validation of the method was done with copper oxidized human low-density lipoprotein (LDL) prepared by ultracentrifugation. In these LDL samples we could identify 46 oxidized molecular phosphatidylcholine species out of 99 possible candidates.
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Affiliation(s)
- Pia Sala
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
- Institute of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse 9/II, Graz 8010, Austria.
| | - Sandra Pötz
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
- Institute of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse 9/II, Graz 8010, Austria.
| | - Martina Brunner
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
| | - Martin Trötzmüller
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
| | - Alexander Fauland
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
- Institute of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse 9/II, Graz 8010, Austria.
| | - Alexander Triebl
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
| | - Jürgen Hartler
- Bioinformatics Group, Institute for Knowledge Discovery, Graz University of Technology, Petersgasse 14, Graz 8010, Austria.
- Omics Center Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
| | - Ernst Lankmayr
- Institute of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse 9/II, Graz 8010, Austria.
| | - Harald C Köfeler
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
- Omics Center Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
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111
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Advances in sample preparation and analytical techniques for lipidomics study of clinical samples. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2014.10.010] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Ahmed Z, Mayr M, Zeeshan S, Dandekar T, Mueller MJ, Fekete A. Lipid-Pro: a computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms. ACTA ACUST UNITED AC 2014; 31:1150-3. [PMID: 25433698 DOI: 10.1093/bioinformatics/btu796] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 11/25/2014] [Indexed: 11/12/2022]
Abstract
UNLABELLED A major challenge for mass spectrometric-based lipidomics, aiming at describing all lipid species in a biological sample, lies in the computational and bioinformatic processing of the large amount of data that arises after data acquisition. Lipid-Pro is a software tool that supports the identification of lipids by interpreting large datasets generated by liquid chromatography--tandem mass spectrometry (LC-MS/MS) using the advanced data-independent acquisition mode MS(E). In the MS(E) mode, the instrument fragments all molecular ions generated from a sample and records time-resolved molecular ion data as well as fragment ion data for every detectable molecular ion. Lipid-Pro matches the retention time-aligned mass-to-charge ratio data of molecular- and fragment ions with a lipid database and generates a report on all identified lipid species. For generation of the lipid database, Lipid-Pro provides a module for construction of lipid species and their fragments using a flexible building block approach. Hence, Lipid-Pro is an easy to use analysis tool to interpret complex MS(E) lipidomics data and also offers a module to generate a user-specific lipid database. AVAILABILITY AND IMPLEMENTATION Lipid-Pro is freely available at: http://www.neurogenetics.biozentrum.uni-wuerzburg.de/en/project/services/lipidpro/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zeeshan Ahmed
- Department of Neurobiology and Genetics, Biocenter, Department of Bioinformatics, Biocenter and Department of Pharmaceutical Biology, Biocenter, University of Wuerzburg, Wuerzburg, Germany Department of Neurobiology and Genetics, Biocenter, Department of Bioinformatics, Biocenter and Department of Pharmaceutical Biology, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Michel Mayr
- Department of Neurobiology and Genetics, Biocenter, Department of Bioinformatics, Biocenter and Department of Pharmaceutical Biology, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Saman Zeeshan
- Department of Neurobiology and Genetics, Biocenter, Department of Bioinformatics, Biocenter and Department of Pharmaceutical Biology, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Thomas Dandekar
- Department of Neurobiology and Genetics, Biocenter, Department of Bioinformatics, Biocenter and Department of Pharmaceutical Biology, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Martin J Mueller
- Department of Neurobiology and Genetics, Biocenter, Department of Bioinformatics, Biocenter and Department of Pharmaceutical Biology, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Agnes Fekete
- Department of Neurobiology and Genetics, Biocenter, Department of Bioinformatics, Biocenter and Department of Pharmaceutical Biology, Biocenter, University of Wuerzburg, Wuerzburg, Germany
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Pinto G, Caira S, Mamone G, Ferranti P, Addeo F, Picariello G. Fractionation of complex lipid mixtures by hydroxyapatite chromatography for lipidomic purposes. J Chromatogr A 2014; 1360:82-92. [DOI: 10.1016/j.chroma.2014.07.093] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 07/27/2014] [Accepted: 07/28/2014] [Indexed: 12/22/2022]
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Sims KH, Tytler EM, Tipton J, Hill KL, Burgess SW, Shaw WA. Avanti lipid tools: connecting lipids, technology, and cell biology. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1841:1038-48. [PMID: 24954118 DOI: 10.1016/j.bbalip.2014.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 05/21/2014] [Accepted: 05/23/2014] [Indexed: 11/15/2022]
Abstract
Lipid research is challenging owing to the complexity and diversity of the lipidome. Here we review a set of experimental tools developed for the seasoned lipid researcher, as well as, those who are new to the field of lipid research. Novel tools for probing protein-lipid interactions, applications for lipid binding antibodies, enhanced systems for the cellular delivery of lipids, improved visualization of lipid membranes using gold-labeled lipids, and advances in mass spectrometric analysis techniques will be discussed. Because lipid mediators are known to participate in a host of signal transduction and trafficking pathways within the cell, a comprehensive lipid toolbox that aids the science of lipidomics research is essential to better understand the molecular mechanisms of interactions between cellular components. This article is part of a Special Issue entitled Tools to study lipid functions.
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Affiliation(s)
- Kacee H Sims
- Avanti Polar Lipids, Inc., 700 Industrial Park Drive, Alabaster, Al 35007, USA.
| | - Ewan M Tytler
- Avanti Polar Lipids, Inc., 700 Industrial Park Drive, Alabaster, Al 35007, USA.
| | - John Tipton
- Avanti Polar Lipids, Inc., 700 Industrial Park Drive, Alabaster, Al 35007, USA.
| | - Kasey L Hill
- Avanti Polar Lipids, Inc., 700 Industrial Park Drive, Alabaster, Al 35007, USA.
| | - Stephen W Burgess
- Avanti Polar Lipids, Inc., 700 Industrial Park Drive, Alabaster, Al 35007, USA.
| | - Walter A Shaw
- Avanti Polar Lipids, Inc., 700 Industrial Park Drive, Alabaster, Al 35007, USA.
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115
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Rožman M, Fabris D, Mrla T, Vukelić Ž. Database and data analysis application for structural characterization of gangliosides and sulfated glycosphingolipids by negative ion mass spectrometry. Carbohydr Res 2014; 400:1-8. [PMID: 25299937 DOI: 10.1016/j.carres.2014.06.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 06/20/2014] [Accepted: 06/27/2014] [Indexed: 01/12/2023]
Abstract
Gangliosides and sulfated glycosphingolipids, as building and functional components of animal cell membranes, participate in cell-to-cell interactions and signaling, but also in changes of cell architecture due to different pathophysiological events. In order to enable higher throughput and to facilitate structural characterization of gangliosides/sulfo-glycosphingolipids (GSL) and their neutral GSL counterparts by negative ion mass spectrometry (MS) and tandem MS techniques, a database and data analysis application have been developed. In silico developed glycosphingolipid database considers a high diversity of ceramide compositions, several sialic acid types (N-acetylneuraminic acid, N-glycolylneuraminic acid and 2-keto-3-deoxynononic acid) as well as possible additional substitutions/modifications of glycosphingolipids, such as O-acetylation, de-N-acetylation, fucosylation, glucuronosylation, sulfation, attachment of repeating terminal hexose-N-acetylhexosamine- (Hex-HexNAc-)1-6 extension, and possible lactone forms. Data analysis application, named GSL-finder, enables correlation of negative ion MS and/or low-energy tandem MS spectra with the database structures. The GSL-database construction and the GSL-finder application searching rules are explained. Validation conducted on GD1a fraction as well as on complex mixtures of native gangliosides isolated from different mammalian brain tissues (human fetal and adult brain, and calf brain tissue) demonstrated agreement with previous studies. Plain, fast, and automated routine for structural characterization of gangliosides/sulfated glycosphingolipids and their neutral GSL counterparts described here could facilitate and improve mass spectrometric analysis of complex glycosphingolipid mixtures originating from variety of normal and pathological biomaterial, where it is known that distinctive changes in glycosphingolipid composition occur.
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Affiliation(s)
- Marko Rožman
- Department of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia.
| | - Dragana Fabris
- Department for Chemistry and Biochemistry, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia.
| | - Tomislav Mrla
- Department of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia.
| | - Željka Vukelić
- Department for Chemistry and Biochemistry, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia.
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116
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Smith R, Mathis AD, Ventura D, Prince JT. Proteomics, lipidomics, metabolomics: a mass spectrometry tutorial from a computer scientist's point of view. BMC Bioinformatics 2014; 15 Suppl 7:S9. [PMID: 25078324 PMCID: PMC4110734 DOI: 10.1186/1471-2105-15-s7-s9] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background For decades, mass spectrometry data has been analyzed to investigate a wide array of research interests, including disease diagnostics, biological and chemical theory, genomics, and drug development. Progress towards solving any of these disparate problems depends upon overcoming the common challenge of interpreting the large data sets generated. Despite interim successes, many data interpretation problems in mass spectrometry are still challenging. Further, though these challenges are inherently interdisciplinary in nature, the significant domain-specific knowledge gap between disciplines makes interdisciplinary contributions difficult. Results This paper provides an introduction to the burgeoning field of computational mass spectrometry. We illustrate key concepts, vocabulary, and open problems in MS-omics, as well as provide invaluable resources such as open data sets and key search terms and references. Conclusions This paper will facilitate contributions from mathematicians, computer scientists, and statisticians to MS-omics that will fundamentally improve results over existing approaches and inform novel algorithmic solutions to open problems.
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117
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Triebl A, Trötzmüller M, Eberl A, Hanel P, Hartler J, Köfeler HC. Quantitation of phosphatidic acid and lysophosphatidic acid molecular species using hydrophilic interaction liquid chromatography coupled to electrospray ionization high resolution mass spectrometry. J Chromatogr A 2014; 1347:104-10. [PMID: 24813932 DOI: 10.1016/j.chroma.2014.04.070] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 03/27/2014] [Accepted: 04/22/2014] [Indexed: 10/25/2022]
Abstract
A method for a highly selective and sensitive identification and quantitation of lysophosphatidic acid (LPA) and phosphatidic acid (PA) molecular species was developed using hydrophilic interaction liquid chromatography (HILIC) followed by negative-ion electrospray ionization high resolution mass spectrometry. Different extraction methods for the polar LPA and PA species were compared and a modified Bligh & Dyer extraction by addition of 0.1M hydrochloric acid resulted in a ≈1.2-fold increase of recovery for the 7 PA and a more than 15-fold increase for the 6 LPA molecular species of a commercially available natural mix compared to conventional Bligh & Dyer extraction. This modified Bligh & Dyer extraction did not show any artifacts resulting from hydrolysis of natural abundant phospholipids. The developed HILIC method is able to separate all PA and LPA species from major polar membrane lipid classes which might have suppressive effects on the minor abundant lipid classes of interest. The elemental compositions of intact lipid species are provided by the high mass resolution of 100,000 and high mass accuracy below 3ppm of the Orbitrap instrument. Additionally, tandem mass spectra were generated in a parallel data dependent acquisition mode in the linear ion trap to provide structural information at molecular level. Limits of quantitation were identified at 45fmol on column and the dynamic range reaches 20pmol on column, covering the range of natural abundance well. By applying the developed method to mouse brain it can be shown that phosphatidic acid contains less unsaturated fatty acids with PA 34:1 and PA 36:1 as the major species. In contrast, for LPA species a high content of polyunsaturated fatty acids (LPA 20:4 and LPA 22:6) was quantified.
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Affiliation(s)
- Alexander Triebl
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Martin Trötzmüller
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria; Omics Center Graz, Stiftingtalstrasse 24, 8010 Graz, Austria.
| | - Anita Eberl
- HEALTH - Institute for Biomedicine and Health Sciences, Joanneum Research Forschungsgesellschaft m.b.H., Graz, Austria
| | - Pia Hanel
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Jürgen Hartler
- Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria; Omics Center Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Harald C Köfeler
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria; Omics Center Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
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118
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Bowden JA, Bangma JT, Kucklick JR. Development of an automated multi-injection shotgun lipidomics approach using a triple quadrupole mass spectrometer. Lipids 2014; 49:609-19. [PMID: 24728931 DOI: 10.1007/s11745-014-3903-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 03/26/2014] [Indexed: 11/26/2022]
Abstract
Shotgun lipidomics is a well-suited approach to monitor lipid alterations due to its ability to scan for varying lipid types on a global, class and individual species level. However, the ability to perform high-throughput shotgun lipidomics has remained challenging due to time-consuming data processing and hardware limitations. To increase the throughput nature of shotgun lipidomics, an automated shotgun lipidomics approach is described utilizing conventional low flow gradient liquid chromatography (LC) analysis (post-injection) coupled with multiple sample injections per sample (on a lipid scan per injection basis). The proposed automated multi-injection approach resulted in a reproducible lipid scanning period of 2.5 min (in a 4.5 min total data acquisition period), thereby providing a sufficient scanning period for performing either mass spectrometric or tandem mass spectrometric analyses. In addition to being simple, robust and reproducible, this approach was also constructed to be cost-effective by using common LC instrumentation and customizable as the data acquisition period can be tailored to perform different scan types, period lengths and scan numbers. Combined with a strategy to create multiple lipid-specific aliquots per sample, the overall approach provides a simple and efficient platform to perform high-throughput lipid profiling.
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Affiliation(s)
- John A Bowden
- Hollings Marine Laboratory, National Institute of Standards and Technology, 331 Fort Johnson Road, Charleston, SC, 29412, USA,
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119
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Ling YS, Liang HJ, Lin MH, Tang CH, Wu KY, Kuo ML, Lin CY. Two-dimensional LC-MS/MS to enhance ceramide and phosphatidylcholine species profiling in mouse liver. Biomed Chromatogr 2014; 28:1284-93. [DOI: 10.1002/bmc.3162] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 01/08/2014] [Accepted: 01/17/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Yee Soon Ling
- Graduate Institute of Toxicology, College of Medicine; National Taiwan University; No. 1, Sec. 1, Jen-ai Rd Taipei 100 Taiwan
- Institute of Environmental Health, College of Public Health; National Taiwan University; No. 17, Xu-zhou Rd Taipei 100 Taiwan
| | - Hao-Jan Liang
- Institute of Environmental Health, College of Public Health; National Taiwan University; No. 17, Xu-zhou Rd Taipei 100 Taiwan
| | - Ming-Huan Lin
- Institute of Occupational Medicine and Industrial Hygiene, College of Public Health; National Taiwan University; No. 17, Xu-zhou Rd Taipei 100 Taiwan
| | - Chuan-Ho Tang
- National Museum of Marine Biology and Aquarium; 2 Houwan Rd, Checheng Pingtung 944 Taiwan
- Institute of Marine Biodiversity and Evolutionary Biology; National Dong Hwa University; 2 Houwan Rd, Checheng Pingtung 944 Taiwan
| | - Kuen-Yuh Wu
- Institute of Occupational Medicine and Industrial Hygiene, College of Public Health; National Taiwan University; No. 17, Xu-zhou Rd Taipei 100 Taiwan
| | - Min-Liang Kuo
- Graduate Institute of Toxicology, College of Medicine; National Taiwan University; No. 1, Sec. 1, Jen-ai Rd Taipei 100 Taiwan
- College of Life Science; National Taiwan University; No. 1, Roosevelt Rd., section 4 Taipei 10617 Taiwan
| | - Ching Yu Lin
- Graduate Institute of Toxicology, College of Medicine; National Taiwan University; No. 1, Sec. 1, Jen-ai Rd Taipei 100 Taiwan
- Institute of Environmental Health, College of Public Health; National Taiwan University; No. 17, Xu-zhou Rd Taipei 100 Taiwan
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120
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Brügger B. Lipidomics: analysis of the lipid composition of cells and subcellular organelles by electrospray ionization mass spectrometry. Annu Rev Biochem 2014; 83:79-98. [PMID: 24606142 DOI: 10.1146/annurev-biochem-060713-035324] [Citation(s) in RCA: 187] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Lipidomics aims to quantitatively define lipid classes, including their molecular species, in biological systems. Lipidomics has experienced rapid progress, mainly because of continuous technical advances in instrumentation that are now enabling quantitative lipid analyses with an unprecedented level of sensitivity and precision. The still-growing category of lipids includes a broad diversity of chemical structures with a wide range of physicochemical properties. Reflecting this diversity, different methods and strategies are being applied to the quantification of lipids. Here, I review state-of-the-art electrospray ionization tandem mass spectrometric approaches and direct infusion to quantitatively assess lipid compositions of cells and subcellular fractions. Finally, I discuss a few examples of the power of mass spectrometry-based lipidomics in addressing cell biological questions.
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Affiliation(s)
- Britta Brügger
- Heidelberg University Biochemistry Center (BZH), 69120 Heidelberg, Germany;
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121
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Knittelfelder OL, Weberhofer BP, Eichmann TO, Kohlwein SD, Rechberger GN. A versatile ultra-high performance LC-MS method for lipid profiling. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 951-952:119-28. [PMID: 24548922 PMCID: PMC3946075 DOI: 10.1016/j.jchromb.2014.01.011] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 01/07/2014] [Accepted: 01/08/2014] [Indexed: 11/17/2022]
Abstract
A new UPLC-based untargeted lipidomic approach using a qTOF hybrid mass spectrometer is introduced. The applied binary gradient enables separations of lipid species including constitutional isomeric compounds and low abundant lipid classes such as phosphatidic acid (PA). Addition of phosphoric acid to the solvents improves peak shapes for acidic phospholipids. MS(E) scans allow simultaneous acquisition of full scan data and collision induced fragmentation to improve identification of lipid classes and to obtain structural information. The method was used to investigate the lipidome of yeast.
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Affiliation(s)
- Oskar L Knittelfelder
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50/II, 8010 Graz, Austria
| | - Bernd P Weberhofer
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50/II, 8010 Graz, Austria
| | - Thomas O Eichmann
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50/II, 8010 Graz, Austria
| | - Sepp D Kohlwein
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50/II, 8010 Graz, Austria
| | - Gerald N Rechberger
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50/II, 8010 Graz, Austria; Omics Center Graz, Austria.
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122
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“Polymeromics”: Mass spectrometry based strategies in polymer science toward complete sequencing approaches: A review. Anal Chim Acta 2014; 808:56-69. [DOI: 10.1016/j.aca.2013.10.027] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 10/07/2013] [Accepted: 10/11/2013] [Indexed: 11/23/2022]
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123
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Chromatographic resolution of closely related species: Separation of warfarin and hydroxylated isomers. J Chromatogr A 2013; 1314:266-75. [DOI: 10.1016/j.chroma.2013.07.092] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 07/19/2013] [Accepted: 07/23/2013] [Indexed: 11/22/2022]
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124
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Comparison of ESI, APCI and MALDI for the (tandem) mass analysis of poly(2-ethyl-2-oxazoline)s with various end-groups. Eur Polym J 2013. [DOI: 10.1016/j.eurpolymj.2013.02.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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125
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Relative quantification of biomarkers using mixed-isotope labeling coupled with MS. Bioanalysis 2013; 4:2525-41. [PMID: 23157360 DOI: 10.4155/bio.12.208] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The identification and quantification of important biomarkers is a critical first step in the elucidation of biological systems. Biomarkers take many forms as cellular responses to stimuli and can be manifested during transcription, translation, and/or metabolic processing. Increasingly, researchers have relied upon mixed-isotope labeling (MIL) coupled with MS to perform relative quantification of biomarkers between two or more biological samples. MIL effectively tags biomarkers of interest for ease of identification and quantification within the mass spectrometer by using isotopic labels that introduce a heavy and light form of the tag. In addition to MIL coupled with MS, a number of other approaches have been used to quantify biomarkers including protein gel staining, enzymatic labeling, metabolic labeling, and several label-free approaches that generate quantitative data from the MS signal response. This review focuses on MIL techniques coupled with MS for the quantification of protein and small-molecule biomarkers.
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126
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Abstract
Lipidomics is defined as a comprehensive analysis of all lipids in a biological system (lipidome). Lipid profiling is a fast-growing area of research due to the involvements of lipids incorporated with human diseases such as obesity, Alzheimer's diseases, and diabetes as well as in drug discovery. Recently improved liquid chromatography and mass spectrometric techniques has provided the rapid expansion of lipidomics research. Lipid extraction and sample preparation is an important step in lipidomics and this chapter describes lipid extractions from different types of samples such as plasma, tissues, yeast, and cells.
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127
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Özbalci C, Sachsenheimer T, Brügger B. Quantitative analysis of cellular lipids by nano-electrospray ionization mass spectrometry. Methods Mol Biol 2013; 1033:3-20. [PMID: 23996167 DOI: 10.1007/978-1-62703-487-6_1] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Lipid analysis performed by nano-electrospray ionization mass spectrometry is a highly sensitive method for quantification of lipids including all lipid species of a given lipid class. Various instrumental setups are used for quantitative lipid analysis, including different modes of ionization, separation, and detection. Here we describe a work-flow for the rapid and quantitative analysis of lipid species from cellular membranes by direct infusion of lipid extracts to a nano-electrospray ionization triple quadrupole/linear ion trap mass spectrometer.
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Affiliation(s)
- Cagakan Özbalci
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
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128
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Hartler J, Tharakan R, Köfeler HC, Graham DR, Thallinger GG. Bioinformatics tools and challenges in structural analysis of lipidomics MS/MS data. Brief Bioinform 2012; 14:375-90. [PMID: 22764120 DOI: 10.1093/bib/bbs030] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Lipidomics, the systematic study of the lipid composition of a cell or tissue, is an invaluable complement to knowledge gained by genomics and proteomics research. Mass spectrometry provides a means to detect hundreds of lipids in parallel, and this includes low abundance species of lipids. Nevertheless, frequently occurring isobaric and isomeric lipid species complicate lipidomics analyses from an analytical and bioinformatics perspective. Various MS/MS strategies have evolved to resolve ambiguous identifications of lipid species, and these strategies have been supported by corresponding bioinformatics analysis tools. This review intends to familiarize readers with available bioinformatics MS/MS analysis tools and databases, the structural information obtainable from these, and their applicability to different MS/MS strategies. Finally, future challenges in detecting double bond positions are investigated from a bioinformatics perspective.
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129
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Hein EM, Hayen H. Comparative Lipidomic Profiling of S. cerevisiae and Four Other Hemiascomycetous Yeasts. Metabolites 2012; 2:254-67. [PMID: 24957378 PMCID: PMC3901198 DOI: 10.3390/metabo2010254] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 02/23/2012] [Accepted: 02/24/2012] [Indexed: 11/16/2022] Open
Abstract
Glycerophospholipids (GP) are the building blocks of cellular membranes and play essential roles in cell compartmentation, membrane fluidity or apoptosis. In addition, GPs are sources for multifunctional second messengers. Whereas the genome and proteome of the most intensively studied eukaryotic model organism, the baker’s yeast (Saccharomyces cerevisiae), are well characterized, the analysis of its lipid composition is still at the beginning. Moreover, different yeast species can be distinguished on the DNA, RNA and protein level, but it is currently unknown if they can also be differentiated by determination of their GP pattern. Therefore, the GP compositions of five different yeast strains, grown under identical environmental conditions, were elucidated using high performance liquid chromatography coupled to negative electrospray ionization-hybrid linear ion trap-Fourier transform ion cyclotron resonance mass spectrometry in single and multistage mode. Using this approach, relative quantification of more than 100 molecular species belonging to nine GP classes was achieved. The comparative lipidomic profiling of Saccharomyces cerevisiae, Saccharomyces bayanus, Kluyveromyces thermotolerans, Pichia angusta, and Yarrowia lipolytica revealed characteristic GP profiles for each strain. However, genetically related yeast strains show similarities in their GP compositions, e.g., Saccharomyces cerevisiae and Saccharomyces bayanus.
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Affiliation(s)
- Eva-Maria Hein
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, D-44227 Dortmund, Germany
| | - Heiko Hayen
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, D-44227 Dortmund, Germany.
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