Automated quantitative analysis of complex lipidomes by liquid chromatography/mass spectrometry

A review of lipidomic technologies applicable to sphingolipidomics and their relevant applications

Sphingolipidomics, a branch of lipidomics, focuses on the large-scale study of the cellular sphingolipidomes. In the current review, two main approaches for the analysis of cellular sphingolipidomes (i.e. LC-MS- or LC-MS/MS-based approach and shotgun lipidomics-based approach) are briefly discussed. Their advantages, some considerations of these methods, and recent applications of these approaches are summarized. It is the authors' sincere hope that this review article will add to the readers understanding of the advantages and limitations of each developed method for the analysis of a cellular sphingolipidome.

Instrument-independent software tools for the analysis of MS-MS and LC-MS lipidomics data

Mass spectrometry (MS), particularly electrospray-MS, is the key tool in modern lipidomics. However, as even a modest scale experiment produces a great amount of data, data processing often becomes limiting. Notably, the software provided with MS instruments are not well suited for quantitative analysis of lipidomes because of the great variety of species present and complexities in response calibration. Here we describe the use of two recently introduced software tools: lipid mass spectrum analysis (LIMSA) and spectrum extraction from chromatographic data (SECD), which significantly increase the speed and reliability of mass spectrometric analysis of complex lipidomes. LIMSA is a Microsoft Excel add-on that (1) finds and integrates the peaks in an imported spectrum, (2) identifies the peaks, (3) corrects the peak areas for overlap by isotopic peaks of other species and (4) quantifies the identified species using included internal standards. LIMSA is instrument-independent because it processes text-format MS spectra. Typically, the analysis of one spectrum takes only a few seconds.The SECD software allows one to display MS chromatograms as two-dimensional maps, which is useful for visual inspection of the data. More importantly, however, SECD allows one to extract mass spectra from user-defined regions of the map for further analysis with, e.g., LIMSA. The use of select regions rather than simple time-range averaging significantly improves the signal-to-noise ratio as signals outside the region of interest are more efficiently excluded. LIMSA and SECD have proven to be robust and convenient tools and are available free of charge from the authors.

Bioinformatics strategies for the analysis of lipids

Owing to their importance in cellular physiology and pathology as well as to recent technological advances, the study of lipids has reemerged as a major research target. However, the structural diversity of lipids presents a number of analytical and informatics challenges. The field of lipidomics is a new postgenome discipline that aims to develop comprehensive methods for lipid analysis, necessitating concomitant developments in bioinformatics. The evolving research paradigm requires that new bioinformatics approaches accommodate genomic as well as high-level perspectives, integrating genome, protein, chemical and network information. The incorporation of lipidomics information into these data structures will provide mechanistic understanding of lipid functions and interactions in the context of cellular and organismal physiology. Accordingly, it is vital that specific bioinformatics methods be developed to analyze the wealth of lipid data being acquired. Herein, we present an overview of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and application of its tools to the analysis of lipid data. We also describe a series of software tools and databases (KGML-ED, VANTED, MZmine, and LipidDB) that can be used for the processing of lipidomics data and biochemical pathway reconstruction, an important next step in the development of the lipidomics field.

The superlattice model of lateral organization of membranes and its implications on membrane lipid homeostasis

Most biological membranes are extremely complex structures consisting of hundreds of different lipid and protein molecules. According to the famous fluid-mosaic model lipids and many proteins are free to diffuse very rapidly in the plane of the membrane. While such fast diffusion implies that different membrane lipids would be laterally randomly distributed, accumulating evidence indicates that in model and natural membranes the lipid components tend to adopt regular (superlattice-like) distributions. The superlattice model, put forward based on such evidence, is intriguing because it predicts that 1) there is a limited number of allowed compositions representing local minima in membrane free energy and 2) those energy minima could provide set-points for enzymes regulating membrane lipid compositions. Furthermore, the existence of a discrete number of allowed compositions could help to maintain organelle identity in the face of rapid inter-organelle membrane traffic.

Lipid profiling of FPLC-separated lipoprotein fractions by electrospray ionization tandem mass spectrometry

Glycerophospholipid and sphingolipid species and their bioactive metabolites are important regulators of lipoprotein and cell function. The aim of the study was to develop a method for lipid species profiling of separated lipoprotein classes. Human serum lipoproteins VLDL, LDL, and HDL of 21 healthy fasting blood donors were separated by fast performance liquid chromatography (FPLC) from 50 microl serum. Subsequently, phosphatidylcholine (PC), lysophosphatidylcholine, sphingomyelin (SM), ceramide (CER), phosphatidylethanolamine (PE), PE-based plasmalogen (PE-pl), cholesterol, and cholesteryl ester (CE) content of the separated lipoproteins was quantified by electrospray ionization tandem mass spectrometry (ESI-MS/MS). Analysis of FPLC fractions with PAGE demonstrated that albumin partially coelutes with HDL fractions. However, analysis of an HDL deficient serum (Tangier disease) showed that only lysophosphatidylcholine, but none of the other lipids analyzed, exhibited a significant coelution with the albumin containing fractions. Approximately 60% of lipoprotein CER were found in LDL fractions and 60% of PC, PE, and plasmalogens in HDL fractions. VLDL, LDL, and HDL displayed characteristic lipid class and species pattern. The developed method provides a detailed lipid class and species composition of lipoprotein fractions and may serve as a valuable tool to identify alterations of lipoprotein lipid species profiles in disease with a reasonable experimental effort.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis of cellular glycerophospholipids enabled by multiplexed solvent dependent analyte-matrix interactions

A matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) based approach was developed for the rapid analyses of cellular glycerophospholipids. Through multiplexed solvent-enabled optimization of analyte-matrix interactions during the crystallization process, over a 30-fold increase in S/N was achieved using 9-aminoacridine as the matrix. The linearity of response (r(2) = 0.99) and dynamic range of this method (over 2 orders of magnitude) were excellent. Moreover, through multiplexing ionization conditions by generating suites of different analyte-matrix interactions in the absence or presence of different alkali metal cations in the matrix, discrete lipid classes were highly and selectively ionized under different conditions resulting in the de facto resolution of lipid classes without chromatography. The resultant decreases in spectral complexity facilitated tandem mass spectrometric analysis through high energy fragmentation of lithiated molecular ions that typically resulted in informative fragment ions. Anionic phospholipids were also detected as singly negatively charged species that could be fragmented using MALDI tandem mass spectrometry leading to structural assignments. Collectively, these results identify a rapid, sensitive, and highly informative MALDI-TOF MS approach for analysis of cellular glycerophospholipids directly from extracts of mammalian tissues without the need for prior chromatographic separation.

Profiling of human urinary phospholipids by nanoflow liquid chromatography/tandem mass spectrometry

Nanoflow liquid chromatography-electrospray ionization-tandem mass spectrometry (nanoLC-ESI-MS-MS) was used for the first time in a comprehensive analysis of human urinary phospholipids (PL). PL mixtures from human urine were separated with a reversed phase LC capillary column coupled to ESI-MS-MS. This study used the dual scan method in which two consecutive LC-ESI-MS-MS runs were done in both positive ion mode to detect phosphatidylcholine (PC) and phosphatidylethanolamine (PE), and in negative ion mode to detect phosphatidylserine (PS), phosphatidylinositol (PI), phosphatidic acid (PA), and phosphatidylglycerol (PG). We focused on identifying the maximum number of PLs from a healthy human urine sample by varying the extracted volume of urine along with the evaluation of extraction efficiency for urinary PLs. We found that 22 PCs, 14 PEs, 15 PIs, 13 PSs, 7 PAs, and 4 PGs were identified during nLC-ESI-MS-MS when phospholipids in urine were extracted by ultracentrifugation. The efficiency of lipid extraction by ultracentrifugation versus lyophilization was evaluated by reducing the initial urine volume. We found that lyophilization was more efficient than ultracentrifugation for extracting lipids from small volumes (1 mL) of urine.

Triacylglycerol fatty acid composition in diet-induced weight loss in subjects with abnormal glucose metabolism--the GENOBIN study

Background

The effect of weight loss on different plasma lipid subclasses at the molecular level is unknown. The aim of this study was to examine whether a diet-induced weight reduction result in changes in the extended plasma lipid profiles (lipidome) in subjects with features of metabolic syndrome in a 33-week intervention.

Methodology/Principal Findings

Plasma samples of 9 subjects in the weight reduction group and 10 subjects in the control group were analyzed using mass spectrometry based lipidomic and fatty acid analyses. Body weight decreased in the weight reduction group by 7.8±2.9% (p<0.01). Most of the serum triacylglycerols and phosphatidylcholines were reduced. The decrease in triacylglycerols affected predominantly the saturated short chain fatty acids. This decrease of saturated short chain fatty acid containing triacylglycerols correlated with the increase of insulin sensitivity. However, levels of several longer chain fatty acids, including arachidonic and docosahexanoic acid, were not affected by weight loss. Levels of other lipids known to be associated with obesity such as sphingolipids and lysophosphatidylcholines were not altered by weight reduction.

Conclusions/Significance

Diet-induced weight loss caused significant changes in global lipid profiles in subjects with abnormal glucose metabolism. The observed changes may affect insulin sensitivity and glucose metabolism in these subjects.

Trial Registration

ClinicalTrials.gov NCT00621205

Microfluidics-based electrospray ionization enhances the intrasource separation of lipid classes and extends identification of individual molecular species through multi-dimensional mass spectrometry: development of an automated high-throughput platform for shotgun lipidomics

Herein, we exploit the use of microfluidics and optimized Taylor cones for improved intrasource separation/selective ionization of lipid classes during electrospray ionization. Increased differential ionization of multiple phospholipid classes was achieved through microfluidics with chip-based ionization resulting in substantial enhancement of intrasource separation/selective ionization of phospholipid classes in comparison to the conventional ion source. For example, using myocardial lipid extracts, 3-fold improvements in intrasource separation/selective ionization of myocardial phospholipid classes were routinely realized in the negative-ion mode in the absence of LiOH or other basic modifiers in the infused sample solutions. Importantly, the relative ratios of ions corresponding to individual molecular species in each lipid class to a selected internal standard from myocardial extracts were nearly identical between the chip-based interface and the syringe-pump-driven capillary interface. Therefore, quantitation of individual lipid molecular species directly from biological extracts through comparisons with internal standards in each lipid class was readily accomplished with an accuracy and dynamic range nearly identical to those documented using the well-established direct syringe-pump-driven capillary interface. Collectively, the use of microfluidics and robotic sample handling substantially enhances intrasource separation of lipids in comparison to routine capillary interfaces and greatly facilitates the use of multi-dimensional mass spectrometry using shotgun lipidomics, thereby providing an automated and high-throughput platform for global analyses of cellular lipidomes.

Affinity-capture tandem mass spectrometric characterization of polyprenyl-linked oligosaccharides: tool to study protein N-glycosylation pathways

N-glycosylation of proteins is recognized as one of the most common post-translational modifications. Until recently it was believed that N-glycosylation occurred exclusively in eukaryotes before the discovery of the general protein glycosylation pathway (Pgl) in Campylobacter jejuni. To date, most techniques to analyze lipid-linked oligosaccharides (LLOs) of these pathways involve the use of radiolabels and chromatographic separation. Technologies capable of characterizing eukaryotic and the newly described bacterial N-glycosylation systems from biologically relevant samples in a quick, accurate, and cost-effective manner are needed. In this paper a new glycomics strategy based on lectin-affinity capture was devised and validated on the C. jejuni N-glycan pathway and the engineered Escherichia coli strains expressing the functional C. jejuni pathway. The lipid-linked oligosaccharide intermediates of the Pgl pathway were then enriched using SBA-agarose affinity-capture and examined by capillary electrophoresis-mass spectrometry (CE-MS). We demonstrate that this method is capable of detecting low levels of LLOs, the sugars are indeed assembled on undecaprenylpyrophosphate, and structural information for expected and unexpected LLOs can be obtained without further sample manipulation. Furthermore, CE-MS analyses of C. jejuni and the E. coli "glyco-factories" showed striking differences in the assembly and control of N-glycan biosynthesis.

A simple and universal method for the separation and identification of phospholipid molecular species

One of the major challenges in lipidomics is to obtain as much information about the lipidome as possible. Here, we present a simple yet universal high-performance liquid chromatography/tandem mass spectrometry (HPLC/MS/MS) method to separate molecular species of all phospholipid classes in one single run. The method is sensitive, robust and allows lipid profiling using full scan mass spectrometry, as well as lipid class specific scanning in positive and negative ionisation mode. This allows high-throughput processing of samples for lipidomics, even if different types of MS analysis are required. Excellent separation of isobaric and even isomeric species is achieved, and original levels of lyso-lipids can be determined without interference from lyso-lipids formed from diacyl species by source fragmentation. As examples of application of this method, more than 400 phospholipid species were identified and quantified in crude phospholipid extracts from rat liver and the parasitic helminth Schistosoma mansoni.

Seasonal acclimatization of brain lipidome in a eurythermal fish (Carassius carassius) is mainly determined by temperature

Crucian carp ( Carassius carassius) is an excellent vertebrate model for studies on temperature adaptation in biological excitable membranes, since the species can tolerate temperatures from 0 to +36°C. To determine how temperature affects the lipid composition of brain, the fish were acclimated for 4 wk at +30, +16, or +4°C in the laboratory, or seasonally acclimatized individuals were captured from the wild throughout the year (temperature = +1 to +23°C), and the brain glycerophospholipid and sphingolipid compositions were analyzed in detail by electrospray-ionization mass spectrometry. Numerous significant temperature-related changes were found in the molecular species composition of the membrane lipids. The most notable and novel finding was a large (∼3-fold) increase of the di-22:6n-3 phosphatidylserine and phosphatidylethanolamine species in the cold. Since the increase of 22:6n-3 in the total fatty acyl pool of the brain was small, the formation of di-22:6n-3 aminophospholipid species appears to be a specific adaptation to low temperature. Such highly unsaturated species could be needed to maintain adequate membrane fluidity in the vicinity of transporters and other integral membrane proteins. Plasmalogens increased somewhat at higher temperatures, possibly to protect membranes against oxidation. The modifications of brain lipidome during the 4-wk laboratory acclimation were, in many respects, similar to those found in the wild, which indicates that the seasonal changes observed in the wild are temperature dependent rather than induced by other environmental factors.

Lipid extraction by methyl-tert-butyl ether for high-throughput lipidomics

Accurate profiling of lipidomes relies upon the quantitative and unbiased recovery of lipid species from analyzed cells, fluids, or tissues and is usually achieved by two-phase extraction with chloroform. We demonstrated that methyl-tert-butyl ether (MTBE) extraction allows faster and cleaner lipid recovery and is well suited for automated shotgun profiling. Because of MTBE's low density, lipid-containing organic phase forms the upper layer during phase separation, which simplifies its collection and minimizes dripping losses. Nonextractable matrix forms a dense pellet at the bottom of the extraction tube and is easily removed by centrifugation. Rigorous testing demonstrated that the MTBE protocol delivers similar or better recoveries of species of most all major lipid classes compared with the "gold-standard" Folch or Bligh and Dyer recipes.

Transbilayer distribution of phospholipids in bacteriophage membranes

We have previously demonstrated that the membranes of several bacteriophages contain more phosphatidylglycerol (PG) and less phosphatidylethanolamine (PE) than the host membrane from where they are derived. Here, we determined the transbilayer distribution of PG and PE in the membranes of bacteriophages PM2, PRD1, Bam35 and phi6 using selective modification of PG and PE in the outer membrane leaflet with sodium periodate or trinitrobenzene sulfonic acid, respectively. In phi6, the transbilayer distributions of PG, PE and cardiolipin could also be analyzed by selective hydrolysis of the lipids in the outer leaflet by phospholipase A(2). We used electrospray ionization mass-spectrometry to determine the transbilayer distribution of phospholipid classes and individual molecular species. In each bacteriophage, PG was enriched in the outer membrane leaflet and PE in the inner one (except for Bam35). Only modest differences in the transbilayer distribution between different molecular species were observed. The effective shape and charge of the phospholipid molecules and lipid-protein interactions are likely to be most important factors driving the asymmetric distribution of phospholipids in the phage membranes. The results of this first systematic study on the phospholipid distribution in bacteriophage membranes will be very helpful when interpreting the accumulating high-resolution data on these organisms.

Quantitative analysis of phosphatidylcholine in rat liver tissue by nanoflow liquid chromatography/tandem mass spectrometry

A quantitative method was developed for the determination of phosphatidylcholine (PC) species concentration using nanoflow LC-ESI-MS/MS. In this study, a calibration method is developed to determine the effect of PC carbon chain length on MS peak intensity. Using the multiple standard addition method, a relationship between the peak intensities of different PC species from nanoflow LC-MS and carbon chain length is established first using different injection amounts of PC standards. From this relationship, a calibration curve for each carbon chain length can be obtained for the concentration calculation. It was found that the MS peak area of PC species analyzed by nanoflow LC-MS linearly decreased with increased acyl carbon numbers, and that the effect of the degree of acyl chain unsaturation on MS peak intensity was minimized when the injection amount was maintained at less than 1 pmol. The method was applied for the quantitative calculation of 34 PC species from rat liver, which were identified from data-dependent MS/MS analysis during nanoflow LC separation.

Analysis of phospholipids by NACE with on-line ESI-MS

A hyphenated method of nonaqueous capillary electrophoresis coupled to electrospray ionization mass spectrometry (NACE-ESI-MS) is described for the simultaneous analysis of phospholipids. The best results were obtained with a mixed solution of methanol/ACN (40:60 v/v) containing 20 mM ammonium acetate and 0.5% acetic acid, under the applied voltage of 30 kV and capillary temperature of 25 degrees C. ESI-MS measurements were performed in the negative mode with methanol/ACN (40:60 v/v) containing 50 mM ammonium acetate as sheath liquid at a flow rate of 2 microL/min. Different phospholipid classes have been successfully separated within 16 min, and the molecular species of every single class have been identified by using MS(2) or MS(3), which generates characteristic fragments through CID. The developed method has been applied to analyze the phospholipids extracted from rat peritoneal surface and the molecular species of phospholipid classes are presented.

Data processing for mass spectrometry-based metabolomics

Modern analytical technologies afford comprehensive and quantitative investigation of a multitude of different metabolites. Typical metabolomic experiments can therefore produce large amounts of data. Handling such complex datasets is an important step that has big impact on extent and quality at which the metabolite identification and quantification can be made, and thus on the ultimate biological interpretation of results. Increasing interest in metabolomics thus led to resurgence of interest in related data processing. A wide variety of methods and software tools have been developed for metabolomics during recent years, and this trend is likely to continue. In this paper we overview the key steps of metabolomic data processing and focus on reviewing recent literature related to this topic, particularly on methods for handling data from liquid chromatography mass spectrometry (LC-MS) experiments.

Sensitive profiling of chemically diverse bioactive lipids

Here, we present an improved method for sensitive profiling of lipids in a single high-performance liquid chromatography-electrospray ionization-quadrupole time of flight mass spectrometry experiment. The approach consists of i) sensitive isocratic elution, which takes advantage of C18 column material that is resistant to increased pH values induced by piperidine, ii) chemometric alignment of mass spectra followed by differential analysis of ion intensities, and iii) semiquantitative analysis of extracted ion chromatograms of interest. A key advantage of this method is its wide applicability to extracts that harbor lipids of considerable chemical complexity. The method allows qualitative and semiquantitative analysis of fatty acyls, glycerophospholipids (such as glycerophosphatidylinositols, glycerophosphatidylserines, and glycerophosphatidylcholines in brain extracts), phosphatidylinositol mannosides, acylated glycerophospholipids, sphingolipids (including ceramides and gangliosides in brain extracts), and, for the first time with ESI, prenols and mycolic acids (MAs). MAs are targets in antimycobacterial therapy, and they play an important immunomodulatory role during host-pathogen interactions. We compared high-resolution mass spectra of MAs derived from Mycobacterium bovis Bacille Camette-Guérin during entry into nonreplicative conditions induced by oxygen deprivation (hypoxic dormancy). Although the overall composition is not drastically altered, there are pronounced differences in individual MAs. alpha-MAs accumulate during entry into dormancy, whereas a subpopulation of keto-MAs is almost entirely eliminated. This effect is reversed upon resuscitation of dormant mycobacteria. These results provide detailed chemical information with relevance to drug development and immunobiology of mycobacteria.

Fatty acid analysis tool (FAAT): An FT-ICR MS lipid analysis algorithm

Electrospray ionization mass spectrometry is becoming an established tool for the investigation of lipids. As the methods for lipid analysis become more mature and their throughput increases, computer algorithms for the interpretation of such data will become a necessity. Toward this end, an algorithm dedicated to the analysis of Fourier transform mass spectral data from lipid extracts has been developed. The algorithm, Fatty Acid Analysis Tool, termed FAAT, has been successfully used to investigate complex lipid extracts containing thousands of components, from various species of mycobacteria including M. tuberculosis and M. abscessus. FAAT is rapid, generally taking tens of seconds to interpret multiple spectra, and accessible to most users as it is implemented in Microsoft Excel Visual Basic Software. In the reduction of data, FAAT begins by scaling spectra (i.e., to account for dilution factors), identifying monoisotopic ions, and assigning isotope packets. Unique features of FAAT include the following: (1) overlapping saturated and unsaturated lipid species can be distinguished, (2) known ions are assigned from a user-defined library including species that possess methylene heterogeneity, (3) and isotopic shifts from stable isotope labeling experiments are identified and assigned (up to a user-defined maximum). In addition, abundance differences between samples grown under normal and stressed conditions can be determined. In the analysis of mycobacterial lipid extracts, FAAT has successfully identified isotopic shifts from incorporation of 15N in M. abscessus. Additionally, FAAT has been used to successfully determine differences in lipid abundances between M. tuberculosis wild-type and mutant strains.

Lipid profiling by multiple precursor and neutral loss scanning driven by the data-dependent acquisition

Data-dependent acquisition of MS/MS spectra from lipid precursors enables to emulate the simultaneous acquisition of an unlimited number of precursor and neutral loss scans in a single analysis. This approach takes full advantage of rich fragment patterns in tandem mass spectra of lipids and enables their profiling by complex (Boolean) scans, in which masses of several fragment ions are considered within a single logical framework. No separation of lipids is required, and the accuracy of identification and quantification is not compromised, compared to conventional precursor and neutral loss scanning.

Bioinformatics strategies for lipidomics analysis: characterization of obesity related hepatic steatosis

Background

Lipids are an important and highly diverse class of molecules having structural, energy storage and signaling roles. Modern analytical technologies afford screening of many lipid molecular species in parallel. One of the biggest challenges of lipidomics is elucidation of important pathobiological phenomena from the integration of the large amounts of new data becoming available.

Results

We present computational and informatics approaches to study lipid molecular profiles in the context of known metabolic pathways and established pathophysiological responses, utilizing information obtained from modern analytical technologies. In order to facilitate identification of lipids, we compute the scaffold of theoretically possible lipids based on known lipid building blocks such as polar head groups and fatty acids. Each compound entry is linked to the available information on lipid pathways and contains the information that can be utilized for its automated identification from high-throughput UPLC/MS-based lipidomics experiments. The utility of our approach is demonstrated by its application to the lipidomic characterization of the fatty liver of the genetically obese insulin resistant ob/ob mouse model. We investigate the changes of correlation structure of the lipidome using multivariate analysis, as well as reconstruct the pathways for specific molecular species of interest using available lipidomic and gene expression data.

Conclusion

The methodology presented herein facilitates identification and interpretation of high-throughput lipidomics data. In the context of the ob/ob mouse liver profiling, we have identified the parallel associations between the elevated triacylglycerol levels and the ceramides, as well as the putative activated ceramide-synthesis pathways.

Novel Application of Reversed-Phase UPLC-oaTOF-MS for Lipid Analysis in Complex Biological Mixtures: A New Tool for Lipidomics

Ultra-Performance LC (UPLC) utilizing sub-2-mum porous stationary phase particles operating with high linear velocities at pressures >9000 psi was coupled with orthogonal acceleration time-of-flight (oaTOF) mass spectrometry and successfully employed for the rapid separation of lipids from complex matrices. The UPLC system produced information-rich chromatograms with typical measured peak widths of 3 s at peak base, generating peak capacities in excess of 200 in 10 min. Further UPLC coupled with MSE technology provided parent and fragment mass information of lipids in one chromatographic run, thus, providing an attractive alternative to current LC methods for targeted lipid analysis as well as lipidomic studies.

Software tools for analysis of mass spectrometric lipidome data

New software tools for quantitative analysis of mass spectrometric lipidome data have been developed. The LIMSA tool finds and integrates peaks in a mass spectrum, matches the peaks with a user-supplied list of expected lipids, corrects for overlap in their isotopic patterns, and quantifies the identified lipid species according to internal standards. Three different algorithms for isotopic correction (deconvolution) were implemented and compared. LIMSA has a convenient user interface and can be applied on any type of MS spectrum. Typically, analysis of one spectrum takes only a few seconds. The SECD tool, designed for analysis of LC-MS data sets, provides an intuitive and informative display of MS chromatograms as two-dimensional "maps" for visual inspection of the data and allows the user to extract mass spectra, to be further analyzed with LIMSA, from arbitrary regions of these maps. More reliable analysis of complex lipidome data with improved signal-to-noise ratio is obtained when compared to standard time-range averaged spectra. The functionality of these tools is demonstrated by analysis of standard mixtures as well as complex biological samples. The tools described here make accurate, high-throughput analysis of extensive sample sets feasible and are made available to the scientific community free of charge.

Altered hepatic lipid status and apolipoprotein A-I metabolism in mice lacking phospholipid transfer protein

The effect of PLTP deficiency on hepatic lipid status and apolipoprotein A-I (apoA-I) biosynthesis in PLTP knockout (PLTP-KO) mice was investigated. PLTP-KO mice exhibited a marked reduction in HDL levels, but also increased triglycerides (TG), phospholipids (PL), and cholesterol in very-low-density lipoproteins (VLDL). Both male and female PLTP-KO mice displayed increased hepatic PL and decreased TG, and in the females, increased hepatic cholesterol was also detected. Primary hepatocytes from PLTP-KO mice displayed a different PL molecular species composition to the wild type (WT) controls, with prominent changes being a reduction of long chain fatty acid-containing and an increase of medium chain mono- or di-unsaturated fatty acid containing PL species. Cultured PLTP-KO hepatocytes synthesized and secreted apoA-I in similar quantities as the WT cells. However, the apoA-I secreted by PLTP-KO hepatocytes contained less choline PL, differing also in phosphatidylcholine/sphingomyelin ratio and fatty acyl species composition when compared to apoA-I from WT hepatocytes. Furthermore, the PLTP-KO-derived PL-deficient apoA-I was less stable in the hepatocyte culture medium than that produced by WT cells. These results demonstrate a complex regulatory role of PLTP in serum and liver lipid homeostasis, as well as in the formation of nascent apoA-I-PL complexes from the liver.

Mass spectrometry-based metabolomics

This review presents an overview of the dynamically developing field of mass spectrometry-based metabolomics. Metabolomics aims at the comprehensive and quantitative analysis of wide arrays of metabolites in biological samples. These numerous analytes have very diverse physico-chemical properties and occur at different abundance levels. Consequently, comprehensive metabolomics investigations are primarily a challenge for analytical chemistry and specifically mass spectrometry has vast potential as a tool for this type of investigation. Metabolomics require special approaches for sample preparation, separation, and mass spectrometric analysis. Current examples of those approaches are described in this review. It primarily focuses on metabolic fingerprinting, a technique that analyzes all detectable analytes in a given sample with subsequent classification of samples and identification of differentially expressed metabolites, which define the sample classes. To perform this complex task, data analysis tools, metabolite libraries, and databases are required. Therefore, recent advances in metabolomics bioinformatics are also discussed.

The lipid maps initiative in lipidomics

The Lipid Metabolites and Pathways Strategy (LIPID MAPS) initiative constitutes the first broad scale national exploration of lipidomics and is supported by a U.S. National Institute of General Medical Sciences Large Scale Collaborative "Glue" Grant. The emerging field of lipidomics faces many obstacles to become a true systems biology approach on par with the other "omics" disciplines. With a goal to overcome these hurdles, LIPID MAPS has been developing the necessary infrastructure and techniques to ensure success. This review introduces a few of the challenges and solutions implemented by LIPID MAPS. Among these solutions is the new comprehensive classification system for lipids, along with a recommended nomenclature and structural drawing representation. This classification system was developed by the International Lipids Classification and Nomenclature Committee (ILCNC) in collaboration with LIPID MAPS and representatives from Europe and Asia. The latest changes implemented by the committee are summarized. In addition, we discuss the adoption of mass spectrometry (MS) as the instrumental platform to investigate lipidomics. This platform has the versatility to quantify known individual lipid molecular species and search for novel lipids affecting biological systems.

Metabolomic approaches to phenotype characterization and applications to complex diseases

Metabolites are the key regulators of systems homeostasis. As such, concentration changes of specific groups of metabolites may reflect systemic responses to environmental, therapeutic or genetic interventions. Thus, the study of metabolites is a powerful tool for the characterization of complex phenotypes as well as for the development of biomarkers for specific physiological responses. Therefore, metabolomics is a valuable platform for studies of complex diseases and the development of new therapies, both in nonclinical disease model characterization and clinical settings.

Overexpression of OSBP-related protein 2 (ORP2) in CHO cells induces alterations of phospholipid species composition

We have previously shown that overexpression of human OSBP-related protein 2 (ORP2) in Chinese hamster ovary (CHO) cells results in increased efflux and reduced esterification of cholesterol. The ORP2-expressing cells also have a reduced level of triacylglycerols. We investigated the effects of ORP2 expression on the phospholipid (PL) molecular species and the neutral lipid (NL) fatty acid composition of CHO cells cultured in the presence or absence of serum lipoproteins. In the presence of lipoproteins, ORP2/CHO cells display an increase in polyunsaturated PL species, and polyunsaturated fatty acids (PUFA) in the diminished NL pool are reduced. The increase of polyunsaturated PL may represent a compensatory response to alterations in cholesterol metabolism. Upon lipoprotein deprivation, the ORP2/CHO cells display a drop in polyunsaturated and an increase in mono and diunsaturated PL species. Our results suggest that this is due to defective recycling of PUFA from the diminished NL pool to PL. Furthermore, the PL PUFA, which are elevated in ORP2/CHO cells, are most likely subject to more rapid turnover than the NL-associated pool. The results provide evidence for a delicate integration of cholesterol, PL, and NL metabolism and a role of ORP2 as a regulator of the cellular lipidome.

Analysis of phospholipid species in rat peritoneal surface layer by liquid chromatography/electrospray ionization ion-trap mass spectrometry

The main phospholipids in rat peritoneal surface layer were analyzed by normal-phase high-performance liquid chromatography (HPLC) coupled with electrospray ionization (ESI) ion-trap mass spectrometry (MS). By using a silica gel column and a gradient of hexane/isopropanol/water as mobile phase containing 5 mmol/L ammonium formate as modifiers, a baseline separation of glycerophosphoehtanolamine (PE), phosphatidylinositol (PI), phosphatidylserine (PS), phosphatidylcholine (PC), sphingomyelin (SM) and lyso-phosphatidylcholine (LPC) was obtained and more than 90 phospholipid constituents in rat peritoneal surface were identified and determined by on-line ion-trap MS detection. The major ethanolamine glycerophospholipids in rat peritoneal surfaces were plasmalogens that were highly enriched in polyunsaturated fatty acids at the sn-2 position. In addition, the fragmentation patterns for each phospholipid class by the ion-trap MS were discussed.

Factors influencing the electrospray intrasource separation and selective ionization of glycerophospholipids

The external electric field induces a separation of cations from negative electrolyte ions in the infusate while differential ionization of molecular species that possess differential electrical propensities can be induced in either the positive- or negative-ion mode during the electrospray ionization process. These physical and electrical processes that occur in the electrospray ion source have been used to selectively ionize lipid classes possessing different electrical propensities that are now known as "intrasource separation and selective ionization". However, the chemical principles underlying charge-dependent alterations in ionization efficiencies responsible for the selective ionization of lipid classes are not known with certainty. Herein, we examined the multiple factors that contribute to intrasource separation and selective ionization of lipid classes under optimal instrumental conditions. We demonstrated that many different lipid classes could be selectively ionized in the ion source and that intrasource resolution of distinct molecular constituents was independent of lipid concentration, flow rate, and residual ions under most experimental conditions. Moreover, the presence of alkaline conditions facilitates the selective ionization of many lipid classes through a mechanism independent of the design of the ESI ion source. Collectively, this study provides an empirical foundation for understanding the chemical mechanisms underlying intrasource separation and selective ionization of lipid classes that can potentially be used for global analysis of cellular lipidomes without the need for chromatographic separation.

Putting the 'Ome' in lipid metabolism

The recognition that altered lipid metabolism underlies many metabolic disorders challenging Western society highlights the importance of this metabolomic subset, herein referred to as the lipidome. Although comprehensive lipid analyses are not a recent concept, the novelty of a lipidomic approach lies with the application of robust statistical algorithms to highlight subtle, yet significant, changes in a population of lipid molecules. First-generation lipidomic studies have demonstrated the sensitivity of interpreting quantitative datasets with computational software; however, the innate power of comprehensive lipid profiling is often not exploited, as robust statistical models are not routinely utilized. Therefore, the current review aims to briefly describe the current technologies suitable for comprehensive lipid analysis, outline innovative mathematical models that have the ability to reveal subtle changes in metabolism, which will ameliorate our understanding of lipid biochemistry, and demonstrate the biological revelations found through lipidomic approaches and their potential implications for health management.

Computer-assisted interpretation of atmospheric pressure chemical ionization mass spectra of triacylglycerols

Current lipidomics approaches require simple and rapid algorithms enabling the interpretation of mass spectra of lipids. Most lipids are complex mixtures of related components in which the composition of the aliphatic fatty acid chains varies from one molecule to the next. Triacylglycerols (TAGs) are an example of such a lipid class. Fatty acid chains are the only parts of the molecule to change from one species to another. Fatty acids, and consequently also TAGs, can be characterized by two parameters; the number of carbon atoms and the number of double bonds. All calculations reflecting relations among ions in the spectra can be easily made using these parameters. An algorithm for the automated interpretation of TAGs from atmospheric pressure chemical ionization mass spectra (TriglyAPCI) is presented in this paper. The algorithm first identifies diacylglycerol fragments and molecular adducts. In the next step, relations among the ions are searched and possible TAG structures are suggested. Individual features of the algorithm are described in detail and the software performance is demonstrated for the liquid chromatography/mass spectrometric (LC/MS) analysis of TAGs isolated from the termite Prorhinotermes canalifrons.

A comprehensive and comparative analysis for MALDI FTMS lipid and phospholipid profiles from biological samples

Described here is a computationally automated method for translating complex accurate mass spectra into biologically relevant and meaningful data. Rapid profiling of detailed high resolution mass spectra resulting from direct analysis of whole cells and tissues by matrix-assisted laser desorption/ionization (MALDI) Fourier transform mass spectrometry (FTMS) is discussed. Lipid and phospholipid ions create complex spectra containing multiple m/z values corresponding to the same fundamental chemical species. A computational approach is employed to sort ions, with mass to charge ratios lower than m/z 1000, into groups of similar lipid and phospholipid compositions for comprehensive and rapid analysis. By sorting or binning ions in this manner, variations in the degree of cation exchange can be avoided, thus increasing the comparability of the data. The result is displayed as a histogram that is easily interpretable and comparable with similar analyses and is particularly useful for direct comparison of similar tissues. Spectra of leaves from a healthy Prunus persica (peach) tree are compared with those from leaves infected by the fungus Taphrina deformans. Although the infection can be seen as a difference in leaf structure and by visual inspection of the mass spectra, the method described here details the chemical difference in phospholipid compositions and their relative abundances.

The emerging field of lipidomics

The crucial role of lipids in cell, tissue and organ physiology is demonstrated by a large number of genetic studies and by many human diseases that involve the disruption of lipid metabolic enzymes and pathways. Examples of such diseases include cancer, diabetes, as well as neurodegenerative and infectious diseases. So far, the explosion of information in the fields of genomics and proteomics has not been matched by a corresponding advancement of knowledge in the field of lipids, which is largely due to the complexity of lipids and the lack of powerful tools for their analysis. Novel analytical approaches--in particular, liquid chromatography and mass spectrometry--for systems-level analysis of lipids and their interacting partners (lipidomics) now make this field a promising area of biomedical research, with a variety of applications in drug and biomarker development.

Mass spectrometric analysis reveals changes in phospholipid, neutral sphingolipid and sulfatide molecular species in progressive epilepsy with mental retardation, EPMR, brain: a case study

Progressive epilepsy with mental retardation, EPMR, belongs to a group of inherited neurodegenerative disorders, the neuronal ceroid lipofuscinoses. The CLN8 gene that underlies EPMR encodes a novel transmembrane protein that localizes to the endoplasmic reticulum (ER) and ER-Golgi intermediate compartment. Recently, CLN8 was linked to a large eukaryotic protein family of TLC (TRAM, Lag1, CLN8) domain homologues with postulated functions in lipid synthesis, transport or sensing. By using liquid chromatography/mass spectrometry we analysed molecular species of major phosholipid and simple sphingolipid classes from cerebral samples of two EPMR patients representing a progressive and advanced state of the disease. The progressive state brain showed reduced levels of ceramide, galactosyl- and lactosylceramide and sulfatide as well as a decrease in long fatty acyl chain containing molecular species within these classes. Among glycerophospholipid classes, an increase in species containing polyunsaturated acyl chains was detected especially in phosphatidylserines and phosphatidylethanolamines. By contrast, saturated and monounsaturated species were overrepresented among phosphatidylserine, phosphatidylethanolamine and phosphatidylinositol classes in the advanced state sample. The observed changes in brain sphingo- and phospholipid molecular profiles may result in altered membrane stability, lipid peroxidation, vesicular trafficking or neurotransmission and thus may contribute to the progression of the molecular pathogenesis of EPMR.