Lipidomics in tissues, cells and subcellular compartments

Mass spectrometry (MS) advances in recent years have revolutionized the biochemical analysis of lipids in plants, and made possible new theories about the structural diversity and functional complexity of lipids in plant cells. Approaches have been developed to profile the lipidome of plants with increasing chemical and spatial resolution. Here we highlight a variety of methods for lipidomics analysis at the tissue, cellular and subcellular levels. These procedures allow the simultaneous identification and quantification of hundreds of lipids species in tissue extracts by direct-infusion MS, localization of lipids in tissues and cells by laser desorption/ionization MS, and even profiling of lipids in individual subcellular compartments by direct-organelle MS. Applications of these approaches to achieve improved understanding of plant lipid metabolism, compartmentation and function are discussed.     

Functional lipidomics: the roles of specialized lipids and lipid-protein interactions in modulating neuronal function

Lipids fulfill multiple specialized roles in neuronal function. In brain, the conduction of electrical impulses, synaptic function, and complex signaling pathways depend on the temporally and spatially coordinated interactions of specialized lipids (e.g., arachidonic acid and plasmalogens), proteins (e.g., ion channels, phospholipases and cyclooxygenases) and integrative lipid-protein interactions. Recent technical advances in mass spectrometry have allowed unparalled insight into the roles of lipids in neuronal function. Through shotgun lipidomics and multidimensional mass spectrometry, in conjunction with the identification of new classes of phospholipases (e.g., calcium dependent and calcium independent intracellular phospholipases), new roles for lipids in cerebral function have been accrued. This review summarizes the advances in our understanding of the types of lipids and phospholipases in the brain and the role of functional lipidomics in increasing our chemical understanding of complex neuronal processes.     

Quantification of 5- and 15-HPETE''s by direct chemical ionization mass spectrometry

This report describes the application of direct chemical ionization mass spectrometry (DCIMS) to the identification and quantification of 5- and 15-HPETEs. A unique feature of the method is use of a polyimide-coated fused silica fiber that allows vaporization of the hydroperoxides, with very low excess energy, into the plume of the chemical ionization reagent gas plasma. Mass spectra are obtained that allow identification of the nonreduced and nonderivatized free acid forms of 5- and 15-HPETE as well as their quantification from 1 microgram to 100 picograms.     

Lipidomics of host-pathogen interactions

The cell biology of intracellular pathogens (viruses, bacteria, eukaryotic parasites) has provided us with molecular information of host-pathogen interactions. As a result it is becoming increasingly evident that lipids play important roles at various stages of host-pathogen interactions. They act in first line recognition and host cell signaling during pathogen docking, invasion and intracellular trafficking. Lipid metabolism is a housekeeping function in energy homeostasis and biomembrane synthesis during pathogen replication and persistence. Lipids of enormous chemical diversity play roles as immunomodulatory factors. Thus, novel biochemical analytics in combination with cell and molecular biology are a promising recipe for dissecting the roles of lipids in host-pathogen interactions.     

Spatial single cell metabolomics: Current challenges and future developments

Single cell metabolomics is a rapidly advancing field of bio-analytical chemistry which aims to observe cellular biology with the greatest detail possible. Mass spectrometry imaging and selective cell sampling (e.g. using nanocapillaries) are two common approaches within the field. Recent achievements such as observation of cell–cell interactions, lipids determining cell states and rapid phenotypic identification demonstrate the efficacy of these approaches and the momentum of the field. However, single cell metabolomics can only continue with the same impetus if the universal challenges to the field are met, such as the lack of strategies for standardisation and quantification, and lack of specificity/sensitivity. Mass spectrometry imaging and selective cell sampling come with unique advantages and challenges which, in many cases are complementary to each other. We propose here that the challenges specific to each approach could be ameliorated with collaboration between the two communities driving these approaches.     

Identification of peripherin as a Akt substrate in neurons

Activation of Akt-mediated signaling pathways is crucial for survival and regeneration of injured neurons. In this study, we attempted to identify novel Akt substrates by using an antibody that recognized a consensus motif phosphorylated by Akt. PC12 cells that overexpressed constitutively active Akt were used. Using two-dimensional PAGE, we identified protein spots that exhibited increased immunostaining of the antibody. Mass spectrometry revealed several major spots as the neuronal intermediate filament protein, peripherin. Using several peripherin fragments, the phosphorylation site was determined as Ser(66) in its head domain in vitro. Furthermore, a co-immunoprecipitation experiment revealed that Akt interacted with the head domain of peripherin in HEK 293T cells. An antibody against phosphorylated peripherin was raised, and induction of phosphorylated peripherin was observed not only in Akt-activated cultured cells but also in nerve-injured hypoglossal motor neurons. These results suggest that peripherin is a novel substrate for Akt in vivo and that its phosphorylation may play a role in motor nerve regeneration.     

Mass spectrometric exploration of phytohormone profiles and signaling networks

Phytohormones have crucial roles in plant growth, development, and acclimation to environmental stress; however, measuring phytohormone levels and unraveling their complex signaling networks and interactions remains challenging. Mass spectrometry (MS) has revolutionized the study of complex biological systems, enabling the comprehensive identification and quantification of phytohormones and their related targets. Here, we review recent advances in MS technologies and highlight studies that have used MS to discover and analyze phytohormone-mediated molecular events. In particular, we focus on the application of MS for profiling phytohormones, elucidating phosphorylation signaling, and mapping protein interactions in plants.     

Quantification of plasma membrane ergosterol of Saccharomyces cerevisiae by direct-injection atmospheric pressure chemical ionization/tandem mass spectrometry

A method for the quantification of ergosterol by atmospheric pressure chemical ionization (APcI) mass spectrometry with direct injection is described. Ergosterol and squalene were ionizable with methanol as the carrier solvent. Using positive-mode tandem mass spectrometry (MS/MS), ergosterol could be identified unambiguously without interference from structurally related compounds such as lanosterol, cholesterol, and squalene. Molecular ions of ergosterol, lanosterol, and cholesterol were detected as the [M + H - H(2)O](+) ion species, while squalene appeared as the [M + H](+) ion species. Upon fragmentation of the three sterols and squalene, the product ion at m/z 69 was present as one of the major fragments in all four compounds. This product ion was used for the quantification of ergosterol in multiple-reaction-monitoring acquisition mode. The relationship between signal intensity and ergosterol concentration was linear over the concentration range of 0.15 to 5 microg/ml, or 7. 56-252 pmol ergosterol per 20 microl injection. The plasma membrane ergosterol of the yeast Saccharomyces cerevisiae could be quantified reproducibly without the need for prior separation from other lipids or derivatization. Six repeated injections of ergosterol standards at concentrations of 0.95 and 4.25 microg/ml gave standard deviations of 0.031 and 0.084, respectively, and coefficients of variation of 3.33 and 1.98%, respectively. The coefficient of variation for the four independently extracted membrane ergosterol samples was 11.18%. The presence of other lipids in a crude lipid extract did not interfere with the ergosterol determination. Direct injection APcI with multiple reaction monitoring is aconvenient and sensitive method for ergosterol quantification requiring no prior fractionation.     

Probing lipid-protein interactions using lipid microarrays

Lipids are central to the regulation and control of several cellular functions. They form many of the important structural features of cells, and are critical members of cellular signal transduction pathways. Cellular dysfunction is often caused by errors in lipid signaling; therefore, the proteins that interact with, synthesize or metabolize the lipids are potential therapeutic targets. Characterizing the contingent of cellular lipids and their abundance and how this is associated with disease will facilitate understanding how to intervene to correct diseases caused by dysfunctional lipid signaling. Since lipid-signaling networks involve several classes of proteins it is essential to determine the identity and role of these proteins in order to understand the networks. These proteins may be receptors, effectors, transporters or enzymes. We present tools, specifically, a lipid microarray platform, to uncover lipid-binding effector proteins that function in lipid signaling pathways. Lipid microarrays will allow researchers to obtain a comparable fingerprint of the proteins from a cell or tissue that bind to lipids, and also enable the identification of functionally important lipid-binding proteins. By applying a systematic approach to the quantification of lipid-protein interactions, lipid microarrays will provide an integrated knowledge base for the human lipidome. These tools have the potential to identify and validate targets to improve personalized medicine and health.     

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

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

Major roles for minor bacterial lipids identified by mass spectrometry

Mass spectrometry of lipids, especially those isolated from bacteria, has ballooned over the past two decades, affirming in the process the complexity of the lipidome. With this has come the identification of new and interesting lipid structures. Here is an overview of several novel lipids, from both Gram-negative and Gram-positive bacteria with roles in health and disease, whose structural identification was facilitated using mass spectrometry. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.     

Algorithms and tools for analysis and management of mass spectrometry data

Mass spectrometry (MS) is a technique that is used for biological studies. It consists in associating a spectrum to a biological sample. A spectrum consists of couples of values (intensity, m/z), where intensity measures the abundance of biomolecules (as proteins) with a mass-to-charge ratio (m/z) present in the originating sample. In proteomics experiments, MS spectra are used to identify pattern expressions in clinical samples that may be responsible of diseases. Recently, to improve the identification of peptides/proteins related to patterns, MS/MS process is used, consisting in performing cascade of mass spectrometric analysis on selected peaks. Latter technique has been demonstrated to improve the identification and quantification of proteins/peptide in samples. Nevertheless, MS analysis deals with a huge amount of data, often affected by noises, thus requiring automatic data management systems. Tools have been developed and most of the time furnished with the instruments allowing: (i) spectra analysis and visualization, (ii) pattern recognition, (iii) protein databases querying, (iv) peptides/proteins quantification and identification. Currently most of the tools supporting such phases need to be optimized to improve the protein (and their functionalities) identification processes. In this article we survey on applications supporting spectrometrists and biologists in obtaining information from biological samples, analyzing available software for different phases. We consider different mass spectrometry techniques, and thus different requirements. We focus on tools for (i) data preprocessing, allowing to prepare results obtained from spectrometers to be analyzed; (ii) spectra analysis, representation and mining, aimed to identify common and/or hidden patterns in spectra sets or in classifying data; (iii) databases querying to identify peptides; and (iv) improving and boosting the identification and quantification of selected peaks. We trace some open problems and report on requirements that represent new challenges for bioinformatics.     

Astrocytes in culture produce anandamide and other acylethanolamides

Anandamide (arachidonylethanolamide) is an endocannabinoid that belongs to the acylethanolamide lipid family. It is produced by neurons in a calcium-dependent manner and acts through cannabinoid CB1 receptors. Other members of the acylethanolamide lipid family are also produced by neurons and act through G-protein-coupled receptors: homo-gamma-linolenylethanolamide (HEA) and docosatetraenylethanolamide (DEA) act through CB1 receptors, palmitylethanolamide (PEA) acts through CB2-like receptors, and oleylethanolamide (OEA) acts through receptors that have not yet been cloned. Although it is clear that anandamide and other acylethanolamides play a major role in neuronal signaling, whether astrocytes also produce these lipids is unknown. We developed a chemical ionization gas chromatography/mass spectrometry method that allows femtomole detection and quantification of anandamide and other acylethanolamides. Using this method, we unambiguously detected and quantified anandamide, HEA, DEA, PEA, and OEA in mouse astrocytes in culture. Stimulation of mouse astrocytes with ionomycin, a calcium ionophore, enhanced the production of anandamide, HEA, and DEA, whereas PEA and OEA levels were unchanged. Endothelin-1, a peptide known to act on astrocytes, enhanced the production of anandamide, without affecting the levels of other acylethanolamides. These results show that astrocytes produce anandamide, HEA, and DEA in a calcium-dependent manner and that anandamide biosynthesis can be selectively stimulated under physiologically relevant conditions. The relative levels of acylethanolamides in astrocytes from rat and human were different from the relative levels of acylethanolamides in mouse astrocytes, indicating that the production of these lipids differs between species. Because astrocytes are known to express CB1 receptors and inactivate endocannabinoids, our finding strongly suggests the existence of a functional endocannabinoid signaling system in these cells.     

Chemical modification of nucleic acids. Methylation of calf thymus DNA investigated by mass spectrometry and liquid chromatography

Mass spectrometry provides an extremely sensitive method for the identification and quantification of modified nucleosides and hence for determining chemical modifications of nucleic acids. When mass spectrometry is used in conjunction with a new high-performance liquid chromatographic system capable of separating 15 methylated and naturally occurring nucleosides, this allows the quantification of products of in vitro DNA methylation. With synthetic (2H3)methyl-labeled methylnucleosides as internal references, the distribution of methylated products formed when calf thymus DNA was reacted with N-methyl-N-nitrosourea(MeNU) was determined. Five modified products, 1-methyldeoxyadenosine(m1dA), 3-methyldeoxycytidine(m3dC), 7-methyldeoxyguanosine(m7dG), 3-methylthymidine(m3T) and O4-methylthymidine(m4T) were detected and the relative distributions were measured. The ability of mass spectrometry/mass spectrometry (tandem mass spectrometry) to increase specificity and sensitivity in this determination is demonstrated and its application to in vivo studies is suggested.     

Targeted lipidomics: fatty acid amides and pain modulation

Mass spectrometric approaches to the identification and quantification of lipid signalling molecules are reviewed. Fatty acid amides are an important new class of lipid signalling molecules which include oleamide, the endocannabinoid anandamide, the endovanilloid/endocannabinoid N-arachidonoyldopamine (NADA) and the endovanilloid N-oleoyldopamine (OLDA) among many others. This diverse group of endogenous compounds comprises combinations of acyl backbones coupled by an amide bond to any of a variety of different small polar molecules such as ethanolamine, various amino acids, and catecholamines. Many fatty acid amides appear to play a role in pain and inflammation. Targeted lipidomics of fatty acid amides aims to identify new members of this diverse class of compounds, of which only a few representative molecules have been characterized to date. This effort has been made feasible by advances in chromatography and mass spectrometry, which permits: (1) identification of compounds present in complex mixtures, (2) astronomical increases in sensitivity due to miniaturization of HPLC components, and (3) novel scanning modes that permit the identification of compounds exhibiting similar structural components. Insofar as lipid signalling molecules such as prostanoids, leukotrienes and endocannabinoids operate via G-protein coupled receptors (GPCR), it appears likely that many of the numerous lipids awaiting identification may serve as ligands for any of the greater than 150 orphan GPCRs.     

Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules

Ligand binding to cell surface receptors initiates a cascade of signaling events regulated by dynamic phosphorylation events on a multitude of pathway proteins. Quantitative features, including intensity, timing, and duration of phosphorylation of particular residues, may play a role in determining cellular response, but experimental data required for analysis of these features have not previously been available. To understand the dynamic operation of signaling cascades, we have developed a method enabling the simultaneous quantification of tyrosine phosphorylation of specific residues on dozens of key proteins in a time-resolved manner, downstream of epidermal growth factor receptor (EGFR) activation. Tryptic peptides from four different EGFR stimulation time points were labeled with four isoforms of the iTRAQ reagent to enable downstream quantification. After mixing of the labeled samples, tyrosine-phosphorylated peptides were immunoprecipitated with an anti-phosphotyrosine antibody and further enriched by IMAC before LC/MS/MS analysis. Database searching and manual confirmation of peptide phosphorylation site assignments led to the identification of 78 tyrosine phosphorylation sites on 58 proteins from a single analysis. Replicate analyses of a separate biological sample provided both validation of this first data set and identification of 26 additional tyrosine phosphorylation sites and 18 additional proteins. iTRAQ fragment ion ratios provided time course phosphorylation profiles for each site. The data set of quantitative temporal phosphorylation profiles was further characterized by self-organizing maps, which resulted in identification of several cohorts of tyrosine residues exhibiting self-similar temporal phosphorylation profiles, operationally defining dynamic modules in the EGFR signaling network consistent with particular cellular processes. The presence of novel proteins and associated tyrosine phosphorylation sites within these modules indicates additional components of this network and potentially localizes the topological action of these proteins. Additional analysis and modeling of the data generated in this study are likely to yield more sophisticated models of receptor tyrosine kinase-initiated signal transduction, trafficking, and regulation.     

脂质组学分析方法进展及其在癌症研究中的应用

脂质占人体内源性代谢物的一半以上,种类繁多,结构复杂,因而具有多种生物功能,与多种生命活动密切相关。脂质组学是代谢组学分支的新兴学科,它可以通过比较不同生理状态下脂质含量的变化,寻找代谢通路中关键的脂质生物标志物,最终揭示脂质在各种生命活动中的作用机制。随着质谱技术的进步,脂质组学在疾病脂类生物标志物的识别、疾病诊断、药物作用机制的研究等方面已展现出广泛的应用前景。本文主要就脂质组学近几年的分析方法进展及其在癌症中的最新应用进行了综述。     

Purification of glycerol dialkyl nonitol tetraether from Sulfolobus acidocaldarius

A modified procedure for extraction and purification of hydrolyzed archaebacterial lipids is described. Lipids were extracted from Sulfolobus acidocaldarius using a Soxhlet extraction procedure followed by trichloroacetic acid solvent-extraction of the residue. The yield of total extractable material by this protocol was 14% which, after a two-phase wash, yielded 10% lipid. Modifications to the published steps for purifying the subsequently hydrolyzed lipids were developed to purify glycerol dialkyl nonitol tetraether (GDNT). The nearly colorless final macrocyclic product was characterized by TLC, IR, NMR, and mass spectrometry.     

Dithranol as a Matrix for Matrix Assisted Laser Desorption/Ionization Imaging on a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer

Mass spectrometry imaging (MSI) determines the spatial localization and distribution patterns of compounds on the surface of a tissue section, mainly using MALDI (matrix assisted laser desorption/ionization)-based analytical techniques. New matrices for small-molecule MSI, which can improve the analysis of low-molecular weight (MW) compounds, are needed. These matrices should provide increased analyte signals while decreasing MALDI background signals. In addition, the use of ultrahigh-resolution instruments, such as Fourier transform ion cyclotron resonance (FTICR) mass spectrometers, has the ability to resolve analyte signals from matrix signals, and this can partially overcome many problems associated with the background originating from the MALDI matrix. The reduction in the intensities of the metastable matrix clusters by FTICR MS can also help to overcome some of the interferences associated with matrix peaks on other instruments. High-resolution instruments such as the FTICR mass spectrometers are advantageous as they can produce distribution patterns of many compounds simultaneously while still providing confidence in chemical identifications. Dithranol (DT; 1,8-dihydroxy-9,10-dihydroanthracen-9-one) has previously been reported as a MALDI matrix for tissue imaging. In this work, a protocol for the use of DT for MALDI imaging of endogenous lipids from the surfaces of mammalian tissue sections, by positive-ion MALDI-MS, on an ultrahigh-resolution hybrid quadrupole FTICR instrument has been provided.