Comparison of electrospray ionization, atmospheric pressure chemical ionization and atmospheric pressure photoionization for a lipidomic analysis of Leishmania donovani

Fatty Acid Composition and Metabolism in Leishmania Parasite Species: Potential Biomarkers or Drug Targets for Leishmaniasis?

Fatty acids have received growing interest in Leishmania biology with the characterization of the enzymes allowing the complete fatty acid synthesis of this trypanosomatid parasite. This review presents a comparative analysis of the fatty acid profiles of the major classes of lipids and phospholipids in different species of Leishmania with cutaneous or visceral tropism. Specificities relating to the parasite forms, resistance to antileishmanial drugs, and host/parasite interactions are described as well as comparisons with other trypanosomatids. Emphasis is placed on polyunsaturated fatty acids and their metabolic and functional specificities, in particular, their conversion into oxygenated metabolites that are inflammatory mediators able to modulate metacyclogenesis and parasite infectivity. The impact of lipid status on the development of leishmaniasis and the potential of fatty acids as therapeutic targets or candidates for nutritional interventions are discussed.

Comparison of Supercritical Fluid Chromatography Hyphenated to an Ultraviolet Detector and Gas Chromatography Hyphenated to a Flame Ionization Detector for Qualitative and Quantitative Analysis of Citrus Essential Oils

A comparison between the classical gas chromatography (GC) technique with supercritical fluid chromatography (SFC) technology was performed using an essential oil of Citrus limon (lemon) as a model, considering its wide use in the cosmetic world. For the qualitative part, the signal annotation was achieved by mass spectrometry using either an electron ionization (EI) or an atmospheric pressure photoionization (APPI) source. For the quantitative part, GC was hyphenated to a flame ionization detector (GC-FID) and SFC to an ultraviolet detector (SFC-UV). The assay of the major component of citrus oil, i.e., limonene, was carried out by SFC-UV. The similar results obtained between GC-FID and SFC-UV allows SFC-UV to be considered as an alternative to GC-FID for Citrus oil characterization. Then, analyses of an essential oil collection from Citrus fruits were achieved to confirm the potential use of SFC-UV for oil classification in the context of quality control of raw materials in cosmetics.

Characterization of effective phytochemicals in traditional Chinese medicine by mass spectrometry

Traditional Chinese medicines (TCMs) have been widely used in clinical and healthcare applications around the world. The characterization of the phytochemical components in TCMs is very important for studying the therapeutic mechanism of TCMs. In the analysis process, sample preparation and instrument analysis are key steps to improve analysis performance and accuracy. In recent years, chromatography combined with mass spectrometry (MS) has been widely used for the separation and detection of trace components in complex TCM samples. This article reviews various sample preparation techniques and chromatography-MS techniques, including the application of gas chromatography-MS and liquid chromatography-MS and other MS techniques in the characterization of phytochemicals in TCM materials and Chinese medicine products. This article also describes a new ambient ionization MS method for rapid and high-throughput analysis of TCM components.

Sequential thermal dissolution of two low-rank coals and characterization of their structures by high-performance liquid chromatography/time-of-flight mass spectrometry and gas chromatography/mass spectrometry

RATIONALE

Gas chromatography/mass spectrometry (GC/MS) and high-performance liquid chromatography/time-of-flight mass spectrometry (HPLC/TOF-MS) were used to separate and reveal the molecular characteristics of organic matter in low-rank coals.

METHODS

Six soluble portions (SPs) were obtained by sequential thermal dissolution (TD) of two low-rank coals in the order of cyclohexane, acetone and methanol solvents at 300°C. Organic matter with different molecular characteristics were enriched in eachTD extract, which was further separated and analyzed by GC/MS and HPLC/TOF-MS using an electrospray ionization source in positive mode to obtain a comprehensive understanding of the structural composition of coals.

RESULTS

Low polarity compounds like alkanes and arenes have a better solubility in cyclohexane. Phorone has the highest relative abundance in the acetone SPs, and the main compounds detected in the methanol SPs are alcohols and phenols. According to the data from HPLC/TOF-MS, most of the oxygen atoms are in the form of carbonyl and alkoxy groups. The nitrogen-containing compounds in SPs are mainly saturated aliphatic amines and pyridines. The sulfur-containing compounds mainly exist in the form of thioalkanes and thiophenes.

CONCLUSIONS

Non-destructive methods were used to obtain soluble matter from coals, and different chromatographic and mass spectrometric techniques were used to separate and analyze the organic matter in coals. Detailed molecular structural information was obtained for the efficient and clean utilization of low-rank coals.

Atmospheric pressure photoionization versus electrospray for the dereplication of highly conjugated natural products using molecular networks

Natural products are sources of inspiration and reservoir of high valuable molecules. Recently, analytical tools based on liquid chromatography coupled to tandem mass spectrometry to generate molecular network became widely employed for dereplication. This strategy greatly accelerates the identification of known and structural hypothesis of unknown. Despite the availability of different ionization sources, alternatives to classical electrospray ionization (ESI), such as atmospheric pressure chemical ionization (APCI) or photoionization (APPI), have been neglected. In particular, APPI has been described for its ionization efficiency on non-polar molecules bearing no acid or basic groups. For that reason, we investigated APPI potential to generate molecular network and compare it to ESI on several criteria that are generation of ion species, sensitivity and signal-to-noise ratio (SNR) for different extracts rich in highly conjugated natural products. We first optimized APPI experimental conditions on crude extract from a fungus, Penicillium sclerotiorum, producing polyketones belonging to the azaphilone family. Then we compared APPI and ESI on different fractions of the fungus and on two plant extracts, French Guyanese Swartzia panacoco (Aubl.) R.S. Cowan (arial parts) and Indian Cassia auriculata L. (leaves) containing phenolic compounds, such as flavonoids. While ESI generated more ion species and displayed a better sensitivity, APPI generated only protonated adduct and better SNR. Comparing ESI and APPI generated species on molecular network reveal that both strategies overlap for the majority of protonated ions.

A complex matrix characterization approach, applied to cigarette smoke, that integrates multiple analytical methods and compound identification strategies for non-targeted liquid chromatography with high-resolution mass spectrometry

RATIONALE

For the characterization of the chemical composition of complex matrices such as tobacco smoke, containing more than 6000 constituents, several analytical approaches have to be combined to increase compound coverage across the chemical space. Furthermore, the identification of unknown molecules requiring the implementation of additional confirmatory tools in the absence of reference standards, such as tandem mass spectrometry spectra comparisons and in silico prediction of mass spectra, is a major bottleneck.

METHODS

We applied a combination of four chromatographic/ionization techniques (reversed-phase (RP) - heated electrospray ionization (HESI) in both positive (+) and negative (-) modes, RP - atmospheric pressure chemical ionization (APCI) in positive mode, and hydrophilic interaction liquid chromatography (HILIC) - HESI positive) using a Thermo Q Exactive™ liquid chromatography/high-resolution accurate mass spectrometry (LC/HRAM-MS) platform for the analysis of 3R4F-derived smoke. Compound identification was performed by using mass spectral libraries and in silico predicted fragments from multiple integrated databases.

RESULTS

A total of 331 compounds with semi-quantitative estimates ≥100 ng per cigarette were identified, which were distributed within the known chemical space of tobacco smoke. The integration of multiple LC/HRAM-MS-based chromatographic/ionization approaches combined with complementary compound identification strategies was key for maximizing the number of amenable compounds and for strengthening the level of identification confidence. A total of 50 novel compounds were identified as being present in tobacco smoke. In the absence of reference MS2 spectra, in silico MS2 spectra prediction gave a good indication for compound class and was used as an additional confirmatory tool for our integrated non-targeted screening (NTS) approach.

CONCLUSIONS

This study presents a powerful chemical characterization approach that has been successfully applied for the identification of novel compounds in cigarette smoke. We believe that this innovative approach has general applicability and a huge potential benefit for the analysis of any complex matrices.

"-Omics" workflow for paleolimnological and geological archives: A review

"-Omics" is a powerful screening method with applications in molecular biology, toxicology, wildlife biology, natural product discovery, and many other fields. Genomics, proteomics, metabolomics, and lipidomics are common examples included under the "-omics" umbrella. This screening method uses combinations of untargeted, semi-targeted, and targeted analyses paired with data mining to facilitate researchers' understanding of the genome, proteins, and small organic molecules in biological systems. Recently, however, the use of "-omics" has expanded into the fields of geology, specifically petrology, and paleolimnology. Specifically, untargeted analyses stand to transform these fields as petroleomics, and sediment-"omics" become more prevalent. "-Omics" facilitates the visualization of small molecule profiles from environmental matrices (i.e. oil and sediment). Small molecule profiles can provide improved understanding of small molecules distributions throughout the environment, and how those compositions can change depending on conditions (i.e. climate change, weathering, etc.). "-Omics" also facilities discovery of next-generation biomarkers that can be used for oil source identification and as proxies for reconstructing past environmental changes. Untargeted analyses paired with data mining and multivariate statistical analyses represents a powerful suite of tools for hypothesis generation, and new method development for environmental reconstructions. Here we present an introduction to "-omics" methodology, technical terms, and examples of applications to paleolimnology and petrology. The purpose of this review is to highlight the important considerations at each step in the "-omics" workflow to produce high quality and statistically powerful data for petrological and paleolimnological applications.

Single-platform ‘multi-omic’ profiling: unified mass spectrometry and computational workflows for integrative proteomics–metabolomics analysis

Advances in instrumentation and analysis tools are permitting evermore comprehensive interrogation of diverse biomolecules and allowing investigators to move from linear signaling cascades to network models, which more accurately reflect the molecular basis of biological systems and processes.

Optimization of normal phase chromatographic conditions for lipid analysis and comparison of associated detection techniques

One important challenge in lipid class analysis is to develop a method suitable or, at least adaptable, for a vast diversity of samples. In the current study, an improved normal-phase liquid chromatography (NPLC) method allowed analyzing the lipid classes present in mammalian, vegetable as well as microorganism (yeast and bacteria) lipid samples. The method effectively separated 30 lipid classes or subclasses with a special focus on medium polarity lipids. The separation was carried out with bare silica stationary phase and was coupled to evaporative light scattering detection (ELSD), charged aerosol detection (Corona-CAD®) and mass spectrometry. Solutions are provided to circumvent technical issues (such as pumping solvents of low viscosity, solvent purity, rinsing step). The influence of mobile phase composition and addition of ionic modifiers on the chromatographic behavior of particular lipid classes is documented. A comparison between ELSD and Corona-CAD® confirmed the interest of this later detector for samples with a wide range of concentration of different lipids. Three common atmospheric pressure ionization interfaces were used for coupling the NPLC separation to a LTQ Velos Pro® mass spectrometer. The comparison of the chromatographic profiles showed that atmospheric pressure chemical ionization (APCI) and atmospheric pressure photoionization (APPI) are both suitable to detect the different lipid classes whereas APPI allows a better sensitivity for lipids at low-concentration.

Lipidomics and anti-trypanosomatid chemotherapy

BACKGROUND

Trypanosomatids such as Leishmania, Trypanosoma brucei and Trypanosoma cruzi belong to the order Kinetoplastida and are the source of many significant human and animal diseases. Current treatment is unsatisfactory and is compromised by the rising appearance of drug resistant parasites. Novel and more effective chemotherapeutics are urgently needed to treat and prevent these devastating diseases, which relies on the identification of essential, parasite specific targets that are absent in the host. Lipids constitute essential components of the cell and carry out multiple critical functions from building blocks of biological membranes to regulatory roles in signal transduction, organellar biogenesis, energy storage, and virulence. The recent technological advances of lipidomics has facilitated the broadening of our knowledge in the field of cellular lipid content, structure, functions, and metabolic pathways.

MAIN BODY

This review highlights the application of lipidomics (i) in the characterization of the lipidome of kinetoplastid parasites or of their subcellular structure(s), (ii) in the identification of unique lipid species or metabolic pathways that can be targeted for novel drug therapies, (iii) as an analytic tool to gain a deeper insight into the roles of specific enzymes in lipid metabolism using genetically modified microorganisms, and (iv) in deciphering the mechanism of action of anti-microbial drugs on lipid metabolism. Lastly, an outlook stating where the field is evolving is presented.

CONCLUSION

Lipidomics has contributed to the expanding knowledge related to lipid metabolism, mechanism of drug action and resistance, and pathogen-host interaction of trypanosomatids, which provides a solid basis for the development of better anti-parasitic pharmaceuticals.

Recent developments in atmospheric pressure photoionization-mass spectrometry

Recent developments in atmospheric pressure photoionization (APPI), which is one of the three most important ionization techniques in liquid chromatography-mass spectrometry, are reviewed. The emphasis is on the practical aspects of APPI analysis, its combination with different separation techniques, novel instrumental developments - especially in gas chromatography and ambient mass spectrometry - and the applications that have appeared in 2009-2014. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:423-449, 2017.

A study of inter-species ion suppression in electrospray ionization-mass spectrometry of some phospholipid classes

Phospholipid quantification in biological samples is crucial and is increasingly studied in lipidomics. Quantitative studies are often performed using commercially available standards of phospholipid classes in order to mimic the composition of biological samples. For this, studies are conducted by liquid chromatography coupled to electrospray ionization-mass spectrometry. In liquid chromatography coupled to mass spectrometry (LC-MS) analysis, the matrix components and the co-elution of several phospholipid species lead to the phenomenon of ion suppression. As a result, a decrease in the response of phospholipid species in mass spectrometry MS is observed. In fact, inter-species ion suppression affects the efficiency of phospholipid (PL) ionization and might also influence the quantitative results. The aim of this work is to study the PL inter-species ion suppression phenomenon in electrospray ionization (ESI)-mass spectrometry on a triple quadrupole TQ and an LTQ-Orbitrap in order to improve quantification in natural and biological samples. Thus, the phospholipid MS response was evaluated to study the effect of acyl chain length, the degree, and the position of unsaturation on acyl chain and the effect of the polar head group structure. A number of saturated and unsaturated phospholipid species and mixtures were analyzed in different ionization modes to a better understanding of inter-species ion suppression phenomenon. PL molecular species responded differently according to the length of fatty acid chains, the number of unsaturation, and the nature of the polar head group. Fatty acid chain length showed to have the most marked effect on MS response.

Liquid chromatography coupled to different atmospheric pressure ionization sources-quadrupole-time-of-flight mass spectrometry and post-column addition of metal salt solutions as a powerful tool for the metabolic profiling of Fusarium oxysporum

Fusarium oxysporum L11 is a non-pathogenic soil-borne fungal strain that yielded an extract that showed antifungal activity against phytopathogens. In this study, reversed-phase high-performance liquid chromatography (RP-HPLC) coupled to different atmospheric pressure ionization sources-quadrupole-time-of-flight mass spectrometry (API-QTOF-MS) was applied for the comprehensive profiling of the metabolites from the extract. The employed sources were electrospray (ESI), atmospheric pressure chemical ionization (APCI) and atmospheric pressure photoionization (APPI). Post-column addition of metal solutions of Ca, Cu and Zn(II) was also tested using ESI. A total of 137 compounds were identified or tentatively identified by matching their accurate mass signals, suggested molecular formulae and MS/MS analysis with previously reported data. Some compounds were isolated and identified by NMR. The extract was rich in cyclic peptides like cyclosporins, diketopiperazines and sansalvamides, most of which were new, and are reported here for the first time. The use of post-column addition of metals resulted in a useful strategy for the discrimination of compound classes since specific adducts were observed for the different compound families. This technique also allowed the screening for compounds with metal binding properties. Thus, the applied methodology is a useful choice for the metabolic profiling of extracts and also for the selection of metabolites with potential biological activities related to interactions with metal ions.

Lipidomics: Novel insight into the biochemical mechanism of lipid metabolism and dysregulation-associated disease

The application of lipidomics, after genomics, proteomics and metabolomics, offered largely opportunities to illuminate the entire spectrum of lipidome based on a quantitative or semi-quantitative level in a biological system. When combined with advances in proteomics and metabolomics high-throughput platforms, lipidomics provided the opportunity for analyzing the unique roles of specific lipids in complex cellular processes. Abnormal lipid metabolism was demonstrated to be greatly implicated in many human lifestyle-related diseases. In this review, we focused on lipidomic applications in brain injury disease, cancer, metabolic disease, cardiovascular disease, respiratory disease and infectious disease to discover disease biomarkers and illustrate biochemical metabolic pathways. We also discussed the analytical techniques, future perspectives and potential problems of lipidomic applications. The application of lipidomics in disease biomarker discovery provides the opportunity for gaining novel insights into biochemical mechanism.

A Functional Group Approach for Prediction of APPI Response of Organic Synthetic Targets

Atmospheric pressure photoionization (APPI) is a technique of choice for ionization of non-polar molecules in mass spectrometry (MS). Reported APPI-based studies tend to focus on a selected compound class, which may contain a variety of functional groups. These studies demonstrate that APPI response frequently differs substantially, indicating a certain dependence on the functional group present. Although this dependence could be employed for APPI response prediction, its systematic use is currently absent. Here, we apply APPI MS to a judiciously-compiled set of 63 compounds containing a number of diverse functional groups commonly utilized in synthesis, reactive functional groups, as well as those containing boron and silicon. Based on the outcome of APPI MS of these compounds, we propose and evaluate a simple guideline to estimate the APPI response for a novel compound, the key properties of which have not been characterized in the gas phase. Briefly, we first identify key functional groups in the compound and gather knowledge on the known ionization energies from the smallest analogues containing said functional groups. We then consider local inductive and resonance effects on said ionization energies for the compounds of interest to estimate the APPI response. Finally, application of APPI MS to compounds of interest considered herein demonstrated extended upper mass ionization limit of 3.5 kDa for non-polymeric compounds.

Non-targeted molecular characterisation of a rose flower ethyl acetate extract using Ultra-HPLC with atmospheric pressure photoionisation and quadrupole time-of-flight MS/MS

INTRODUCTION

A non-targeted approach to characterise the phytochemical composition of the flower organ of an original rose cultivar 'Jardin de Granville'® was developed. Particular attention was paid to the less documented molecular families of intermediate polarity, compared with the polyphenol family (anthocyanins, flavonoids, tannins) and volatile compounds.

OBJECTIVE

To develop a molecular fingerprinting method for the rapid qualitative phytochemical characterisation of the rose flower ethyl acetate extract.

MATERIAL AND METHODS

An ultra-HPLC with atmospheric pressure photoionisation (APPI) and quadrupole time-of-flight (QTOF) MS/MS combined with microwave-assisted extraction was carried out for ethyl acetate extracts as an intermediate polarity extraction solvent in order to obtain the most exhaustive extract containing a large range of molecular families. An optimised methodology based on the coupling of the UHPLC and APPI source with a QTOF analyser was developed to characterise the extracted molecules.

RESULTS

Sixty-one compounds were identified in the extract, covering eight molecular families of intermediate polarity ranging from polyphenols to triglycerides. The presence of flavonoids with anti-oxidant properties and of triterpenoids with potential anti-inflammatory activity was evidenced and cell-wall constituents such as fatty acids, glycolipids, sphingolipids and acylated sterol glycosides were characterised. Some chlorophyll derivatives were also detected.

CONCLUSION

The method developed is appropriate for fast phytochemical evaluation of rose ethyl acetate extract. It produced accurate mass and MS/MS spectra, which permitted identification of a wide range of compounds of intermediate polarity.

Lipidomics of Alzheimer’s disease

Alzheimer’s disease (AD) is a progressive brain disease that leads to an irreversible loss of neurons and cognition. It is the most common cause of dementia and can be considered as a major public health problem. At the histological level, AD is characterized by senile plaques and neurofibrillary tangles. Numerous studies involving genomic, transcriptomic and proteomic approaches have been published in order to understand the molecular mechanisms involved in AD, and to find new biomarkers. Metabolomics, and in particular lipidomics, have recently offered new possibilities due to the development of robust and sensitive analytical methods, such as LC–MS. This review aims to illustrate how lipidomics can help understand the biological mechanisms inherent to AD and how lipids can be considered as relevant biomarkers of AD at early stages.

Two birds with one stone: doing metabolomics with your proteomics kit

Proteomic research facilities and laboratories are facing increasing demands for the integration of biological data from multiple ‘-OMICS’ approaches. The aim to fully understand biological processes requires the integrated study of genomes, proteomes and metabolomes. While genomic and proteomic workflows are different, the study of the metabolome overlaps significantly with the latter, both in instrumentation and methodology. However, chemical diversity complicates an easy and direct access to the metabolome by mass spectrometry (MS). The present review provides an introduction into metabolomics workflows from the viewpoint of proteomic researchers. We compare the physicochemical properties of proteins and peptides with metabolites/small molecules to establish principle differences between these analyte classes based on human data. We highlight the implications this may have on sample preparation, separation, ionisation, detection and data analysis. We argue that a typical proteomic workflow (nLC-MS) can be exploited for the detection of a number of aliphatic and aromatic metabolites, including fatty acids, lipids, prostaglandins, di/tripeptides, steroids and vitamins, thereby providing a straightforward entry point for metabolomics-based studies. Limitations and requirements are discussed as well as extensions to the LC-MS workflow to expand the range of detectable molecular classes without investing in dedicated instrumentation such as GC-MS, CE-MS or NMR.

Lipidomics applications in health, disease and nutrition research

The structural and functional diversity of lipids accounts for their involvement into a wide range of homeostatic processes and disease states, including lifestyle-related diseases as well as genetic conditions. Challenges presented by this diversity have been addressed to a great extent by the development of lipidomics, a platform that makes possible the detailed profiling and characterisation of lipid species present in any cell, organelle, tissue or body fluid, and allows for a wider appreciation of the biological role of lipid networks. Progress in the field of lipidomics has been greatly facilitated by recent advances in MS and includes a range of analytical platforms supporting applications spanning from qualitative and quantitative assessment of multiple species to lipid imaging. Here we review these MS techniques currently in routine use in lipidomics, alongside with new ones that have started making an impact in the field. Recent applications in health, disease and nutrition-related questions will also be discussed with a view to convey the importance of lipidomics contributions to biosciences and food technology.

On the future of mass-spectrometry-based lipidomics

Lipids have highly diverse functions that go beyond cellular membrane structure and energy storage. One of the great challenges in lipid research will be to understand how the enormous complexity of lipid homeostasis is maintained. Genetic approaches combined with mass spectrometry-based lipidomics will help to elucidate how cells create and maintain their nonrandom lipid distribution within tissues, cells, organelles and lipid bilayers. Lipid homeostasis is crucial for many cellular processes and we are currently only beginning to understand the specific functions of lipids and the local environment that they create.