The Application of Chemometrics in Metabolomic and Lipidomic Analysis Data Presentation for Halal Authentication of Meat Products

The halal status of meat products is an important factor being considered by many parties, especially Muslims. Analytical methods that have good specificity for the authentication of halal meat products are important as quality assurance to consumers. Metabolomic and lipidomic are two useful strategies in distinguishing halal and non-halal meat. Metabolomic and lipidomic analysis produce a large amount of data, thus chemometrics are needed to interpret and simplify the analytical data to ease understanding. This review explored the published literature indexed in PubMed, Scopus, and Google Scholar on the application of chemometrics as a tool in handling the large amount of data generated from metabolomic and lipidomic studies specifically in the halal authentication of meat products. The type of chemometric methods used is described and the efficiency of time in distinguishing the halal and non-halal meat products using chemometrics methods such as PCA, HCA, PLS-DA, and OPLS-DA is discussed.     

Sample Preparation Methods for Lipidomics Approaches Used in Studies of Obesity

Obesity is associated with alterations in the composition and amounts of lipids. Lipids have over 1.7 million representatives. Most lipid groups differ in composition, properties and chemical structure. These small molecules control various metabolic pathways, determine the metabolism of other compounds and are substrates for the syntheses of different derivatives. Recently, lipidomics has become an important branch of medical/clinical sciences similar to proteomics and genomics. Due to the much higher lipid accumulation in obese patients and many alterations in the compositions of various groups of lipids, the methods used for sample preparations for lipidomic studies of samples from obese subjects sometimes have to be modified. Appropriate sample preparation methods allow for the identification of a wide range of analytes by advanced analytical methods, including mass spectrometry. This is especially the case in studies with obese subjects, as the amounts of some lipids are much higher, others are present in trace amounts, and obese subjects have some specific alterations of the lipid profile. As a result, it is best to use a method previously tested on samples from obese subjects. However, most of these methods can be also used in healthy, nonobese subjects or patients with other dyslipidemias. This review is an overview of sample preparation methods for analysis as one of the major critical steps in the overall analytical procedure.     

Enantioselectivity in Drug Pharmacokinetics and Toxicity: Pharmacological Relevance and Analytical Methods

Enzymes, receptors, and other binding molecules in biological processes can recognize enantiomers as different molecular entities, due to their different dissociation constants, leading to diverse responses in biological processes. Enantioselectivity can be observed in drugs pharmacodynamics and in pharmacokinetic (absorption, distribution, metabolism, and excretion), especially in metabolic profile and in toxicity mechanisms. The stereoisomers of a drug can undergo to different metabolic pathways due to different enzyme systems, resulting in different types and/or number of metabolites. The configuration of enantiomers can cause unexpected effects, related to changes as unidirectional or bidirectional inversion that can occur during pharmacokinetic processes. The choice of models for pharmacokinetic studies as well as the subsequent data interpretation must also be aware of genetic factors (such as polymorphic metabolic enzymes), sex, patient age, hepatic diseases, and drug interactions. Therefore, the pharmacokinetics and toxicity of a racemate or an enantiomerically pure drug are not equal and need to be studied. Enantioselective analytical methods are crucial to monitor pharmacokinetic events and for acquisition of accurate data to better understand the role of the stereochemistry in pharmacokinetics and toxicity. The complexity of merging the best enantioseparation conditions with the selected sample matrix and the intended goal of the analysis is a challenge task. The data gathered in this review intend to reinforce the importance of the enantioselectivity in pharmacokinetic processes and reunite innovative enantioselective analytical methods applied in pharmacokinetic studies. An assorted variety of methods are herein briefly discussed.     

High-Performance Nucleic Acid Sensors for Liquid Biopsy Applications

Circulating tumour nucleic acids (ctNAs) are released from tumours cells and can be detected in blood samples, providing a way to track tumors without requiring a tissue sample. This “liquid biopsy” approach has the potential to replace invasive, painful, and costly tissue biopsies in cancer diagnosis and management. However, a very sensitive and specific approach is required to detect relatively low amounts of mutant sequences linked to cancer because they are masked by the high levels of wild-type sequences. This review discusses high-performance nucleic acid biosensors for ctNA analysis in patient samples. We compare sequencing- and amplification-based methods to next-generation sensors for ctDNA and ctRNA (including microRNA) profiling, such as electrochemical methods, surface plasmon resonance, Raman spectroscopy, and microfluidics and dielectrophoresis-based assays. We present an overview of the analytical sensitivity and accuracy of these methods as well as the biological and technical challenges they present.     

Screening of microdialysates taken before and after induced liver damage; on-line solid phase extraction-electrospray ionization-mass spectrometry

A novel method is described to follow known and unknown compounds in biological processes using microdialysis sampling and mass spectrometric detection. By implementation of internal standard, desalting/enrichment for the sample work-up, and multivariate data analysis, this methodology is a basis for future applications in early diagnosis of diseases and organ damage, as a complement to the routinely used clinical methods for biological samples. The present study includes screening without specific target analytes, of samples collected by microdialysis from liver of anaesthetized rats before and after local damage to this organ. Sample series were classified by principal component analysis, and the stimulation was identified in the chemical patterns produced by the presented analytical tool.     

High‐Performance Nucleic Acid Sensors for Liquid Biopsy Applications

Circulating tumour nucleic acids (ctNAs) are released from tumours cells and can be detected in blood samples, providing a way to track tumors without requiring a tissue sample. This “liquid biopsy” approach has the potential to replace invasive, painful, and costly tissue biopsies in cancer diagnosis and management. However, a very sensitive and specific approach is required to detect relatively low amounts of mutant sequences linked to cancer because they are masked by the high levels of wild‐type sequences. This review discusses high‐performance nucleic acid biosensors for ctNA analysis in patient samples. We compare sequencing‐ and amplification‐based methods to next‐generation sensors for ctDNA and ctRNA (including microRNA) profiling, such as electrochemical methods, surface plasmon resonance, Raman spectroscopy, and microfluidics and dielectrophoresis‐based assays. We present an overview of the analytical sensitivity and accuracy of these methods as well as the biological and technical challenges they present.     

Infrared and Raman imaging of biological and biomimetic samples

Established methods for imaging of biological or biomimetic samples, such as fluorescence and optical microscopy, magnetic resonance imaging (MRI), X-ray tomography or positron emission tomography (PET) are currently complemented by infrared (both near-IR and mid-IR) as well as Raman spectroscopic imaging, whether it be on a microscopic or macroscopic scale. These vibrational spectroscopic techniques provide a wealth of information without a priori knowledge of either the spectral data or the composition of the sample. Infrared radiation does not harm the organism, no electric potential needs to be applied, and the measurements are not influenced by electromagnetic fields. In addition, no extrinsic labeling or staining, which may perturb the system under investigation, has to be added. The immense volume of information contained in spectroscopic images requires multivariate analysis methodologies in order to effectively mine the chemical and spatial information contained within the data as well as to analyze a time-series of images in order to reveal the origin of a chemical or biochemical process. The promise and limitations of this new analytical tool are surveyed in this review.     

Surveying selenium speciation from soil to cell—forms and transformations

The aim of this review is to present and evaluate the present knowledge of which selenium species are available to the general population in the form of food and common supplements and how these species are metabolized in mammals. The overview of the selenium sources takes a horizontal approach, which encompasses identification of new metabolites in yeast and food of plant and animal origin, whereas the survey of the mammalian metabolism takes a horizontal as well as a vertical approach. The vertical approach encompasses studies on dynamic conversions of selenium compounds within cells, tissues or whole organisms. New and improved sample preparation, separation and detection methods are evaluated from an analytical chemical perspective to cover the progress in horizontal speciation, whereas the analytical methods for the vertical speciation and the interpretations of the results are evaluated from a biological angle as well.     

Automation and Standardization—A Coupled Approach towards Reproducible Sample Preparation Protocols for Nanomaterial Analysis

Whereas the characterization of nanomaterials using different analytical techniques is often highly automated and standardized, the sample preparation that precedes it causes a bottleneck in nanomaterial analysis as it is performed manually. Usually, this pretreatment depends on the skills and experience of the analysts. Furthermore, adequate reporting of the sample preparation is often missing. In this overview, some solutions for techniques widely used in nano-analytics to overcome this problem are discussed. Two examples of sample preparation optimization by automation are presented, which demonstrate that this approach is leading to increased analytical confidence. Our first example is motivated by the need to exclude human bias and focuses on the development of automation in sample introduction. To this end, a robotic system has been developed, which can prepare stable and homogeneous nanomaterial suspensions amenable to a variety of well-established analytical methods, such as dynamic light scattering (DLS), small-angle X-ray scattering (SAXS), field-flow fractionation (FFF) or single-particle inductively coupled mass spectrometry (sp-ICP-MS). Our second example addresses biological samples, such as cells exposed to nanomaterials, which are still challenging for reliable analysis. An air–liquid interface has been developed for the exposure of biological samples to nanomaterial-containing aerosols. The system exposes transmission electron microscopy (TEM) grids under reproducible conditions, whilst also allowing characterization of aerosol composition with mass spectrometry. Such an approach enables correlative measurements combining biological with physicochemical analysis. These case studies demonstrate that standardization and automation of sample preparation setups, combined with appropriate measurement processes and data reduction are crucial steps towards more reliable and reproducible data.     

Tandem Mass Spectrometry Imaging Enables High Definition for Mapping Lipids in Tissues

Mass spectrometry imaging (MSI) of lipids in biological tissues is useful for correlating molecular distribution with pathological results, which could provide useful information for both biological research and disease diagnosis. It is well understood that the lipidome could not be clearly deciphered without tandem mass spectrometry analysis, but this is challenging to achieve in MSI due to the limitation in sample amount at each image spot. Here we develop a multiplexed MS² imaging (MS²I) method that can provide MS² images for 10 lipid species or more for each sampling spot, providing spatial structural lipidomic information. Coupling with on-tissue photochemical derivatization, imaging of 20 phospholipid C=C location isomers is also realized, showing enhanced molecular images with high definition in structure for mouse brain and human liver cancer tissue sections. Spatially mapped t-distributed stochastic neighbor embedding has also been adopted to visualize the tumor margin with enhancement by structural lipidomic information.     

Analytical method development and validation of anticancer agent, 5-fluorouracil,and its metabolites in biological matrices: An updated review

Abstract

5-fluorouracil (5-FU) refers to a fluorinated pyrimidine analogue that has been widely used as an anticancer agent for colon, head, and neck cancers. Detection of 5-FU and its metabolites; 5-fluorouridine and 5-fluoro-2-deoxyuridine in biological samples allows optimization of pharmacotherapy and encourages fundamental investigations of this medication. The development of accurate and reliable sample preparation, as well as analytical methods, is critical to isolate targeted analytes from complex matrices, apart from increasing detection sensitivity of analytes. With that, this paper presents a review of prior studies pertaining to chromatographic and electrophoretic methods that focused on the analysis of 5-FU and its metabolites in biological matrices such as plasma and urine. This paper concentrates on HPLC, GC and CE systems, which are the most commonly used strategies for analytical separation of 5-FU and its metabolites from samples. Detection of these antineoplastic agents at trace level demands highly sensitive and selective analytical methodologies. Application of these analytical techniques to biological matrices is reviewed with a focus on method development strategies, including types of mobile phases and background electrolytes employed in LC and CE systems.     

Analysis of bile acids in human biological samples by microcolumn separation techniques: A review

Bile acids are a group of compounds essential for lipid digestion and absorption with a steroid skeleton and a carboxylate side chain usually conjugated to glycine or taurine. Bile acids are regulatory molecules for a number of metabolic processes and can be used as biomarkers of various disorders. Since the middle of the twentieth century, the detection of bile acids has evolved from simple qualitative analysis to accurate quantification in complicated mixtures. Advanced methods are required to characterize and quantify individual bile acids in these mixtures. This article overviews the literature from the last two decades (2000–2020) and focuses on bile acid analysis in various human biological samples. The methods for sample preparation, including the sample treatment of conventional (blood plasma, blood serum, and urine) and unconventional samples (bile, saliva, duodenal/gastric juice, feces, etc.) are shortly discussed. Eventually, the focus is on novel analytical approaches and methods for each particular biological sample, providing an overview of the microcolumn separation techniques, such as high-performance liquid chromatography, gas chromatography, and capillary electrophoresis, used in their analysis. This is followed by a discussion on selected clinical applications.     

Determination of metals in biofluids and tissues: sample preparation methods for atomic spectroscopic techniques

Several sample preparation methods unique to each instrumental technique exist for the elemental analysis of biological specimens, but no review or book has dealt with them. The present review is an attempt to fill this void and focuses on sample preparation methods unique to atomic and X-ray spectroscopic techniques. The techniques covered are: flame and electrothermal AAS, inductively coupled plasma atomic emission spectrometry (ICP-AES), inductively coupled plasma mass spectrometry (ICP-MS) and X-ray fluorescence spectrometry (XRF) since these are most commonly used in trace element analysis of biological materials. The intent is not to present the procedural details for the various tissues or elements, but rather to highlight the methods which are unique to each instrument. The bibliography accompanying this review should aid the analytical chemist in his/her search for the detailed preparation protocols.     

Photoinduced spectrofluorimetric determination of fluoroquinolones in human urine by using three- and two-way spectroscopic data and multivariate calibration

Multivariate methods comprise of a group of chemometric tools allowing the analysis of different analytical data, i.e., spectroscopic, chromatographic obtained from multichannel detector systems. Second-way data are widely used in analytical applications in combination with multivariate calibration methods, but three- and higher-way data are yet not as widely applied. In complex biological samples, the employment of the three-way data is of special interest, as they may be combined with methods that exploit the second-order advantage allowing calculating individual concentrations of the analytes of interest in the presence of unknown interferences in untreated samples. A very sensitive and selective method is proposed, by coupling photoinduced fluorescence and multivariate analysis of the three-way data excitation-emission fluorescence matrices (EEMs), of the photoproducts obtained from UV irradiation of three fluoroquinolones: enoxacin (ENO), norfloxacin (NOR) and ofloxacin (OFLO). The application of a previous photoirrradiation process allows the determination of mixtures of ENO, NOR and OFLO, in urine samples at biological levels without sample pretreatments. The resolution ability of N-way partial least squares (N-PLS), parallel factor analysis (PARAFAC) and self weighted alternating trilinear decomposition (SWATLD), is compared with partial least squares (PLS) and unfolded-PLS (U-PLS), in the analysis of ENO, NOR and OFLO in human urine samples.     

Organic ion imaging of biological tissue with secondary ion mass spectrometry and matrix-assisted laser desorption/ionization

Organic secondary ion mass spectrometry (SIMS) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry can be used to produce molecular images of samples. This is achieved through ionization from a clearly identified point on a flat sample, and performing a raster of the sample by moving the point of ionization over the sample surface. The unique analytical capabilities of mass spectrometry for mapping a variety of biological samples at the tissue level are discussed. SIMS provides information on the spatial distribution of the elements and low molecular mass compounds as well as molecular structures on these compounds, while MALDI yields spatial information about higher molecular mass compounds, including their distributions in tissues at very low levels, as well as information on the molecular structures of these compounds. Application of these methods to analytical problems requires appropriate instrumentation, sample preparation methodology, and a data presentation usually in a three-coordinate plot where x and y are physical dimensions of the sample and z is the signal amplitude. The use of imaging mass spectrometry is illustrated with several biological systems.     

Modern analytical techniques in metabolomics analysis

Metabolomics is the comprehensive assessment of endogenous metabolites and attempts to systematically identify and quantify metabolites from a biological sample. Small-molecule metabolites have an important role in biological systems and represent attractive candidates to understand disease phenotypes. Metabolites represent a diverse group of low-molecular-weight structures including lipids, amino acids, peptides, nucleic acids, organic acids, vitamins, thiols and carbohydrates, which makes global analysis a difficult challenge. The recent rapid development of a range of analytical platforms, including GC, HPLC, UPLC, CE coupled to MS and NMR spectroscopy, could enable separation, detection, characterization and quantification of such metabolites and related metabolic pathways. Owing to the complexity of the metabolome and the diverse properties of metabolites, no single analytical platform can be applied to detect all metabolites in a biological sample. The combined use of modern instrumental analytical approaches has unravelled the ideal outcomes in metabolomics, and is beneficial to increase the coverage of detected metabolites that can not be achieved by single-analysis techniques. Integrated platforms have been frequently used to provide sensitive and reliable detection of thousands of metabolites in a biofluid sample. Continued development of these analytical platforms will accelerate widespread use and integration of metabolomics into systems biology. Here, the application of each hyphenated technique is discussed and its strengths and limitations are discussed with selected illustrative examples; furthermore, this review comprehensively highlights the role of integrated tools in metabolomic research.     

Recent advances in miniaturisation--the role of microchip electrophoresis in clinical analysis

This review aims to highlight the current role of microchip CE (MCE) in clinical analysis to date, and also its future potential in this important area. One of the most notable advancements in separation science, which has accelerated in the last decade, has been the use of plastic and glass microchips to achieve high-speed electrophoresis separations in seconds, requiring only pico or nanolitre sample volumes. So far, in the clinical laboratory, MCE has lent itself to the resolution of very complex challenging analytes such as DNA, RNA, protein analysis, cellular components and other disease biomarkers. At present, most basic clinical laboratories rely heavily upon various kinds of enzymatic immunoassays as these methods offer speed, specificity, reliability and are well established analytical methods. However, this is not always the case, as with all analytical methods there are limitations, and sometimes enzymatic-based assays can be challenged by low-level concentration of target analytes present in samples resulting in high RSD values and results that cannot be interpreted. In some cases, this difficulty can be exasperated when complex sample matrices are presented for analysis, and interfering components result in highly exaggerated results from unwanted extra enzymatic binding. MCE may have a role in providing alternative highly sophisticated automated clinical analysis using state-of-the-art methodologies.     

An Overview of the Analytical Methods for the Determination of Organic Ultraviolet Filters in Cosmetic Products and Human Samples

UV filters are a group of compounds commonly used in different cosmetic products to absorb UV radiation. They are classified into a variety of chemical groups, such as benzophenones, salicylates, benzotriazoles, cinnamates, p-aminobenzoates, triazines, camphor derivatives, etc. Different tests have shown that some of these chemicals are absorbed through the skin and metabolised or bioaccumulated. These processes can cause negative health effects, including mutagenic and cancerogenic ones. Due to the absence of official monitoring protocols, there is an increased number of analytical methods that enable the determination of those compounds in cosmetic samples to ensure user safety, as well as in biological fluids and tissues samples, to obtain more information regarding their behaviour in the human body. This review aimed to show and discuss the published studies concerning analytical methods for the determination of organic UV filters in cosmetic and biological samples. It focused on sample preparation, analytical techniques, and analytical performance (limit of detection, accuracy, and repeatability).     

Evaluation of different warping methods for the analysis of CE profiles of urinary nucleosides

Nowadays, numerous metabolite concentrations can readily be determined in a given biological sample by high-throughput analytical methods. However, such raw analytical data comprise noninformative components due to many disturbances normally occurring in the analyses of biological material. To eliminate those unwanted original analytical data components, advanced chemometric data preprocessing methods might be of help. Here, such methods are applied to electrophoretic nucleoside profiles in urine samples of cancer patients and healthy volunteers. In this study, three warping methods: dynamic time warping (DTW), correlation optimized warping (COW), and parametric time warping (PTW) were examined on two sets of electrophoretic data by means of quality of peaks alignment, time of preprocessing, and way of customization. The application of warping methods helped to limit shifting of peaks and enabled differentiation between whole electropherograms of healthy and cancer patients objectively by a principal component analysis (PCA). The evaluation of preprocessed data and raw data by PC analysis confirms differences between the applied warping tools and proves their suitability in metabonomic data interpretation.     

Classification of the biological material with use of FTIR spectroscopy and statistical analysis

Rapid detection and discrimination of dangerous biological materials such as bacteria and their spores has become a security aim of considerable importance. Various analytical methods, including FTIR spectroscopy combined with statistical analysis have been used to identify vegetative bacteria, bacterial spores and background interferants. The present work discusses the application of FTIR technique performed in reflectance mode using Horizontal Attenuated Total Reflectance accessory (HATR) to the discrimination of biological materials. In comparison with transmission technique the HATR is more rapid and do not require the sample destruction, simultaneously giving similar absorbance bands. HATR-FTIR results combined with statistical analysis PCA and HCA demonstrate that this combination provides novel and accurate microbial identification technique.