Metabolic profiling for the identification of Huntington biomarkers by on‐line solid‐phase extraction capillary electrophoresis mass spectrometry combined with advanced data analysis tools

In this work, an untargeted metabolomic approach based on sensitive analysis by on‐line solid‐phase extraction capillary electrophoresis mass spectrometry (SPE‐CE‐MS) in combination with multivariate data analysis is proposed as an efficient method for the identification of biomarkers of Huntington's disease (HD) progression in plasma. For this purpose, plasma samples from wild‐type (wt) and HD (R6/1) mice of different ages (8, 12, and 30 weeks), were analyzed by C₁₈‐SPE‐CE‐MS in order to obtain the characteristic electrophoretic profiles of low molecular mass compounds. Then, multivariate curve resolution alternating least squares (MCR‐ALS) was applied to the multiple full scan MS datasets. This strategy permitted the resolution of a large number of metabolites being characterized by their electrophoretic peaks and their corresponding mass spectra. A total number of 29 compounds were relevant to discriminate between wt and HD plasma samples, as well as to follow‐up the HD progression. The intracellular signaling was found to be the most affected metabolic pathway in HD mice after 12 weeks of birth, when mice already showed motor coordination deficiencies and cognitive decline. This fact agreed with the atrophy and dysfunction of specific neurons, loss of several types of receptors, and changed expression of neurotransmitters.     

Metabolomics of transgenic maize combining Fourier transform-ion cyclotron resonance-mass spectrometry,capillary electrophoresis-mass spectrometry and pressurized liquid extraction

In this work, the potential of combining capillary electrophoresis-time-of-flight-mass spectrometry (CE-TOF-MS) and Fourier transform-ion cyclotron resonance-mass spectrometry (FT-ICR-MS) for metabolomics of genetically modified organisms (GMOs) is demonstrated. Thus, six different varieties of maize, three of them transgenic (PR33P66 Bt, Tietar Bt and Aristis Bt) and their corresponding isogenic lines (PR33P66, Tietar and Aristis) grown under the same field conditions, were analyzed. Based on the ultrahigh resolution and remarkable mass accuracy provided by the 12-T FT-ICR-MS it was possible to directly analyze a good number of metabolites whose identity could be proposed based on their specific isotopic pattern. For identification of metabolite isomers, CE-TOF-MS was also used combining the information on nominal mass with electrophoretic mobility corroborating in that way the identity of several new biomarkers. Furthermore, PLE extractions were evaluated in order to establish selective extraction as an additional criterion to obtain useful information in maize metabolomics. Differences in the metabolite levels were found between the three transgenic maize varieties compared with their wild isogenic lines in some specific metabolic pathways. To our knowledge, this is the first time that an approach as the one presented in this work (pressurized liquid extraction + FT-ICR-MS + CE-TOF-MS) is shown for a metabolomic study.     

Design and Application of an Easy to Use Oligonucleotide Mass Calculation Program

With the development of new synthesis procedures, an ever increasing number of chemical modifications can now be incorporated into synthetic oligonucleotides, representing new challenges for analytical chemists to efficiently identify and characterize such molecules. While conventional mass spectrometry (MS) has proven to be a powerful tool to study nucleic acids, new and improved methods and software are now needed to address this emerging challenge. In this report, we describe a simple yet powerful program that affords great flexibility in the calculation of theoretical masses for conventional as well as modified oligonucleotide molecules. This easy to use program can accept input oligonucleotide sequences and then calculate the theoretical mass values for full length products, process impurities, potential metabolites, and gas phase fragments. We intentionally designed this software so that modified nucleotide residues can be incorporated into oligonucleotide sequences, and corresponding mass values can be rapidly calculated. To test the utility of this program, two oligonucleotides that contain a large number of chemical modifications were synthesized. We have analyzed these samples using a Q-TOF mass spectrometer and compared the calculated masses to the observed ones. We found that all of the data matched very well with less than 30 ppm mass errors, well within the expectation for our instrument operated in its current mode. These data confirmed the validity of calculations performed with this new software.

Detection and expression analysis of recombinant proteins in plant-derived complex mixtures using nanoUPLC-MS(E)

The use of mass spectrometry to identify recombinant proteins that are expressed in total soluble proteins (TSPs) from plant extracts is necessary to accelerate further processing steps. For example, the method consists of TSP sample preparation and trypsin digestion prior to the preliminary characterization using nanoUPLC-MS(E) analysis of the recombinant proteins that are expressed in TSP samples of transgenic soybean seeds. A TSP sample as small as 50 μg can be effectively analyzed. In this study, transgenic soybean seeds that expressed recombinant cancer testis antigen (CTAG) were used. The procedure covered 30% of the protein sequence and was quantified at 0.26 ng, which corresponded to 0.1% of the TSP sample. A comparative proteomic profile was generated by the comparison of a negative control and sample that showed a unique expression pattern of CTAG in a transgenic line. The experimental data from the TSP extraction, sample preparation and data analysis are discussed herein.     

Ultra-high performance liquid chromatography tandem mass spectrometry for comprehensive analysis of urinary acylcarnitines

We report an enabling mass spectrometric method for the analysis of lipid metabolites in order to define better the lipid metabolome in terms of chemical diversity and generate fragment ion spectra of these metabolites as a potential resource for unknown metabolite identification. This work focuses on the analysis of one important class of lipid metabolites, the acylcarnitines. Current analytical methods have only detected and identified a limited number of these metabolites. The method described herein provides the most comprehensive acylcarnitine profile in urine of healthy individuals up to date. It involves an optimized solid phase extraction technique for selective analyte extraction using cartridges containing both lipophilic and cation-exchange properties. The captured analytes are then subjected to ultra-high performance liquid chromatography (UPLC) separation, followed by tandem mass spectrometry (MS/MS) analysis using information-dependent acquisitions and selected reaction monitoring (SRM). The urine of six healthy individuals was analyzed using this method. A total of 355 acylcarnitines were detected; only 43 of them have been previously reported in the urine of healthy individuals. Detection of this large number of acylcarnitines illustrates the great diversity of the lipid metabolome as well as the usefulness of the method for profiling acylcarnitines. Furthermore, the MS/MS spectra of the 355 acylcarnitines will be uploaded to a public human metabolome database as a mass spectrometric resource for unknown metabolite identification.     

Thin-layer detection of diazepam and/or chilordiazepoxide alone or in combination with major drugs of abuse in drug abuse urine screening programs

Three extraction procedures for the detection of diazepam, oxazepam, chlorazepate and/or chlordiazepoxide in human urines are presented. All three procedures are based on the acid hydrolysis of benzodiazepines and/or their conjugated metabolites to give the corresponding benzophenones. Procedure I involves the direct acid hydrolysis of raw urine and is recommended when the aim is to test the abuse of benzodiazepine derivatives only. Procedure II Is a two-step extraction method in which a wide variety of drugs of abuse including cocaine (test based on the detection of benzoylecgonine) are extracted by the first step using paper loaded with cation-exchange resin and the benzodiazepines are tested in the second step by the acid hydrolysis of the spent urine left after removing the ion-exchange paper. Procedure III involves the use of inert fibrous matrix and then its acid hydrolysis. The detection procedure is based on the identification of methylaminochlorobenzophenone (MACB) and aminochlorobenzophenone (ACB). MACB is detected as a yellow-colored compound while ACB is detected by spraying with Bratton-Marshall reagent. Specificity of detection of ACB has been achieved by the selection of a thin-layer developing solvent system in which sulfonamides with primary aromatic amino groups remain at the origin.     

Evaluation of soybean seed protein extraction focusing on metalloprotein analysis

Two methods of protein extraction for soybean seeds were evaluated in terms of preservation of the metal ions bound to proteins after the extraction and separation procedures. The proteins were firstly separated according to their molar masses by polyacrylamide gel electrophoresis. Then, the protein bands were mapped by synchrotron radiation X-ray fluorescence in order to establish which metal ions were present in each one. Finally, some mapped protein bands were decomposed by microwave-assisted combustion and Ca, Cu, K, Mg, Mn, and Zn were quantified by inductively coupled plasma mass spectrometry or inductively coupled plasma optical emission spectrometry. The extraction methods studied were Method A (based on the treatment of ground soybean seeds with hexane and their extraction with Tris–HCl and β-mercaptoethanol) and Method B (based on the treatment of ground soybean seeds with petroleum ether and their extraction with Tris–HCl, dithiothreitol, phenylmethanesulfonyl fluoride, sodium dodecyl sulfate and potassium chloride). The best method was Method B, in which a 78% higher extraction efficiency was obtained when compared to Method A. Additionally, the metal-protein interactions were more appropriately preserved when Method B was applied, where the most affected ions were those that are bound weakly to proteins, such as Ca, K, and Mg.     

Combined data mining strategy for the systematic identification of sport drug metabolites in urine by liquid chromatography time-of-flight mass spectrometry

The development of comprehensive methods able to tackle with the systematic identification of drug metabolites in an automated fashion is of great interest. In this article, a strategy based on the combined use of two complementary data mining tools is proposed for the screening and systematic detection and identification of urinary drug metabolites by liquid chromatography full-scan high resolution mass spectrometry. The proposed methodology is based on the use of accurate mass extraction of diagnostic ions (compound-dependent information) from in-source CID fragmentation without precursor ion isolation along with the use of automated mass extraction of accurate-mass shifts corresponding to typical biotransformations (non compound-dependent information) that xenobiotics usually undergo when metabolized. The combined strategy was evaluated using LC–TOFMS with a suite of nine sport drugs representative from different classes (propranolol, bumetanide, clenbuterol, ephedrine, finasteride, methoxyphenamine, methylephedrine, salbutamol and terbutaline), after single doses administered to rats. The metabolite identification coverage rate obtained with the systematic method (compared to existing literature) was satisfactory, and provided the identification of several non-previously reported metabolites. In addition, the combined information obtained helps to minimize the number of false positives. As an example, the systematic identification of urinary metabolites of propranolol enabled the identification of up to 24 metabolites, 15 of them non previously described in literature, which is a valuable indicator of the usefulness of the proposed systematic procedure.     

Analysis of amicarbazone and its two metabolites in grains and soybeans by liquid chromatography with tandem mass spectrometry

A sensitive, simple and reliable analytical method based on a modified quick, easy, cheap, effective, rugged, safe sample preparation and liquid chromatography with tandem mass spectrometry detection was developed for the simultaneous determination of amicarbazone and its two major metabolites desamino amicarbazone and isopropyl‐2‐hydroxy‐desamino amicarbazone residues in grains (rice, wheat, corn, buckwheat) and soybean. Several parameters, including liquid chromatography and tandem mass spectrometry conditions, extraction approaches and the adsorbents for clean‐up, which might influence the accuracy of the method, were extensively investigated. The established method was further validated by determining the linearity (R² > 0.99), fortified recovery (79–118%), precision (1–12%) and sensitivity (limit of quantification, 5 μg/kg for amicarbazone and desamino amicarbazone, and 10 μg/kg for isopropyl‐2‐hydroxy‐desamino amicarbazone). Finally, the established method was successfully applied to determine the residues of amicarbazone and its metabolites in 49 real samples of grain and soybean.     

Analysis of Polyphenols in Honey: Extraction,Separation and Quantification Procedures

Polyphenols are secondary plant metabolites playing a major role as potentially functional components. They can also be used for honey authentication. This review gathers the recent literature references about honey extraction procedures, as well as instrumental analysis of phenolic compounds found in honey. Liquid-Liquid extraction is widely used for both extraction and purification purposes, with adequate recovery percentages. However, the use of high solvent volumes is a major disadvantage. More environmentally friendly methods include accelerated solvent extraction, and dispersive and inverse dispersive liquid-liquid microextraction. Solid phase extraction is the most common method for honey polyphenols’ isolation. Polyphenol isolation by a combination of liquid-liquid and solid phase extraction allows good recoveries for a variety of different compounds. High-performance liquid chromatography with ultraviolet or mass spectrometry detectors is by far, the most commonly employed instrumental procedure to separate and quantify polyphenols in honey although capillary electrophoresis has been also successfully used for these purposes. The use of new sorbents, the optimization of current procedures and the development of other simple and rapid analytical techniques are challenges for future analysis of polyphenols found in honey.     

Optimization of harvesting, extraction, and analytical protocols for UPLC-ESI-MS-based metabolomic analysis of adherent mammalian cancer cells

In this study, a liquid chromatography mass spectrometry (LC/MS)-based metabolomics protocol was optimized for quenching, harvesting, and extraction of metabolites from the human pancreatic cancer cell line Panc-1. Trypsin/ethylenediaminetetraacetic acid (EDTA) treatment and cell scraping in water were compared for sample harvesting. Four different extraction methods were compared to investigate the efficiency of intracellular metabolite extraction, including pure acetonitrile, methanol, methanol/chloroform/H₂O, and methanol/chloroform/acetonitrile. The separation efficiencies of hydrophilic interaction chromatography (HILIC) and reversed-phase liquid chromatography (RPLC) with UPLC-QTOF-MS were also evaluated. Global metabolomics profiles were compared; the number of total detected features and the recovery and relative extraction efficiencies of target metabolites were assessed. Trypsin/EDTA treatment caused substantial metabolite leakage proving it inadequate for metabolomics studies. Direct scraping after flash quenching with liquid nitrogen was chosen to harvest Panc-1 cells which allowed for samples to be stored before extraction. Methanol/chloroform/H₂O was chosen as the optimal extraction solvent to recover the highest number of intracellular features with the best reproducibility. HILIC had better resolution for intracellular metabolites of Panc-1 cells. This optimized method therefore provides high sensitivity and reproducibility for a variety of cellular metabolites and can be applicable to further LC/MS-based global metabolomics study on Panc-1 cell lines and possibly other cancer cell lines with similar chemical and physical properties.

Simplified procedures for the determination of fenoldopam and its metabolites in human plasma by high-performance liquid chromatography with electrochemical detection: comparison of manual and robotic sample preparation methods

Quantitative analytical methods, based on high-performance liquid chromatography with electrochemical detection, were developed for fenoldopam and its metabolites in human plasma. Two extraction methods, a liquid-liquid extraction method for fenoldopam and its methoxy metabolites and a liquid-solid extraction procedure for the sulfate and glucuronide conjugates of fenoldopam were developed. The extractions can either be performed manually or by robot. The limit of detection for fenoldopam, its sulfate and methoxy metabolites was 0.025, 2 and 0.5 ng/ml, respectively, at a signal to noise ratio of 4. The intra-assay and inter-assay coefficients of variation for both manual and robotic extraction procedures were comparable. These methods were suitably selective and sensitive for pharmacokinetic and metabolic studies of fenoldopam.     

Solid phase extraction system for vitamin D and its major metabolites in human plasma

A new procedure using C18 and silica cartridges for the extraction and subsequent separation of vitamin D and its major metabolites from plasma has been developed and compared to a conventional extraction procedure with respect to lipophilic material extracted as evaluated by high-performance liquid chromatographic profiles. The C18 cartridges were efficient in extracting all compounds tested while subsequent chromatography of the extract on silica cartridges was effective in resolving vitamin D and its metabolites based on increasing polarity. High-performance liquid chromatographic profiles of each silica cartridge fraction clearly demonstrated that the newly conceived solid phase extraction was superior to conventional extraction methods with respect to cleanliness of sample fractions. This difference in lipophilic load between the new and conventional extraction systems was most apparent in the vitamin D and 25-hydroxyvitamin D containing fractions. The new extraction system can be used when total extraction and subsequent analysis of vitamin D and its major metabolites is desired.     

Investigation of the continuous flow of the sample solution on the performance of electromembrane extraction: Comparison with conventional procedure

In this study, electromembrane extraction from a flowing sample solution, termed as continuous‐flow electromembrane extraction, was developed and compared with conventional procedures for the determination of four basic drugs in real samples. Experimental parameters affecting the extraction efficiency were further studied and optimized. Under optimum conditions, linearity of continuous‐flow procedure was within 8.0–500 ng/mL, while it was wider for conventional procedures (2.0–500 ng/mL). Moreover, repeatability (percentage relative standard deviation) was found to range between 5.6 and 10.4% (n  = 3) for the continuous‐flow procedure, with a better repeatability than that of conventional procedures (2.3–5.5% (n  = 3)). Also, for the continuous‐flow procedure, the estimated detection limit (signal‐to‐noise ratio = 3) was less than 2.4 ng/mL and extraction recoveries were within 8–10%, while the corresponding figures for conventional procedures were less than 0.6 ng/mL and 42–60%, respectively. Thus, the results showed that both continuous flow and conventional procedures were applicable for the extraction of model compounds. However, the conventional procedure was more convenient to use, and thus it was applied to determine sample drugs in real urine and wastewater samples.     

Metabolomics study of cured tobacco using liquid chromatography with mass spectrometry: Method development and its application in investigating the chemical differences of tobacco from three growing regions

Cured tobacco is an important plant material. Component studies are a big challenge for its significantly diverse chemical properties and vastly different concentrations. In this work, liquid chromatography with quadrupole time‐of‐flight mass spectrometry was used to perform a metabolomics study of cured tobacco owing to its efficient separation and detection of semipolar metabolites. A solvent of methanol/water (8:2, v/v) and 30 min of ultrasound time were found to be optimal to perform extraction. 95, 92, and 93% of metabolite features had within 20% of coefficient of variation for repeatability, intraday and interday precision analysis, respectively, indicating a good stability of the method developed. 113 metabolites were identified in cured tobacco based on accurate mass, retention time, and MS/MS fragments. The developed method was applied to a metabolomics study of cured tobacco from three growing regions. Forty three metabolites were found to be contributed to the classification. It is shown that the developed method can be applied to metabolomics analysis of plant materials.     

Comparison of Solid-Phase Extraction and Liquid-Liquid Extraction Methods for Liquid Chromatographic Determination of Diltiazem and its Metabolites in Plasma

Abstract

A rapid solid-phase extraction method for the determination of diltiazem and its metabolites from plasma was compared to a conventional liquid-liquid extraction procedure we have described previously. Analytical recovery for all compounds was greater than 90 % for solid-phase extraction whereas for liquid-liquid extraction, mean recovery ranged from 67 to 82 %. The increase of extraction efficiency was closely related to an improvement of the detection limit for the metabolites. Solid phase extraction procedure was found to be more convenient, rapid and sensitive than liquid-liquid extraction and represents a useful analytical tool for the monitoring of diltiazem and its metabolites in clinical investigations.     

Comparison of single extraction procedures,using either conventional shaking or microwave heating,and the Tessier sequential extraction method for the fractionation of heavy metals from environmental samples

The conventional four-step sequential extraction method and the EDTA and acetic acid single extraction procedures were applied to sewage sludge and sediment samples. The results obtained with these samples for Cu, Cr, Ni, Pb and Zn using the Tessier method were compared with those supplied by the two single extraction procedures employed. In addition, the Tessier method was also applied to a reference material, CRM 483, and these results were also compared with the certified EDTA and acetic acid values for this sample. As a result, good agreement was found between the metal contents released in the first three fractions of the Tessier method and those leached by the simpler single extraction procedures for the most of the elements studied. Subsequently, the conventional EDTA and acetic acid extraction methods were accelerated by means of microwave energy, in order to reduce the operating time. The extraction efficiency of the first three fractions of the Tessier method was compared with that obtained using the optimised microwave single extraction procedures and only in sewage sludge and CRM 483 samples were satisfactory results found for all the elements studied, except Cr and Pb. This means that the microwave single extraction procedures optimised in this work could be employed as screening methods to evaluate rapidly the easiest mobilizable heavy metals in these samples, although more samples should be analysed to determine their general applicability. The application of the accelerated single extraction procedures to a reference material, CRM 483, provided satisfactory results for all the elements studied, except for Cr in both methods and for Pb in the acetic acid extracts.     

Determination of pesticides and their degradation products in soil: critical review and comparison of methods

Pesticides are applied widely to protect plants from disease, weeds and insect damage, and usually come into contact with soil, where they undergo a variety of transformations that provide a complex pattern of metabolites. This article reviews the most relevant analytical methods for determining pesticides and their transformation products in soils. We address some recent advances in sampling and sample-preparation technologies for soil analysis. We discuss and critically evaluate procedures, such as liquid extraction methods (pressurized liquid extraction or microwave-assisted extraction) and solid-phase based methods (headspace solid-phase microextraction, solid-phase microextraction or matrix-solid-phase dispersion). Analysis of pesticides is generally carried out by gas chromatography (GC) or liquid chromatography (LC) coupled to different detectors, especially to mass spectrometers (MSs). However, alternative and/or complementary methods, using capillary electrophoresis (CE), biosensors and bioassays have emerged recently. We also consider the advantages and the disadvantages of the various methodologies.     

Development of a solid phase extraction protocol coupled with liquid chromatography mass spectrometry to analyze central carbon metabolites in lake sediment microcosms

An ion exchange solid phase extraction (SPE) strategy is developed for application with liquid chromatography-tandem quadrupole mass spectrometry (LC-MS/MS) for characterization of central carbon metabolites involved in methane assimilation and adjacent pathways in natural mixtures. For this purpose, short-time microcosm samples were obtained from lake sediment known to consume methane. Three SPE procedures were developed for the recovery of 51 targeted metabolites from five compound classes (amino acids, carboxylic acids, sugar phosphates, nucleotides and acyl-CoAs). The three SPE procedures employed were mixed mode (i) strong cation exchange, (ii) strong anion exchange and (iii) weak anion exchange. By spiking stable isotopic labeled standards, validation of the SPE procedures for the sediment extracts demonstrated that a 3 cm(3), 60 mg SPE sorbent bed provided effective loading capacity for targeted metabolites with an analytical variation of 16% RSD. We readily analyzed 32 of the targeted 51 metabolites using LC-MS/MS after sediment sample extraction, cleanup and pre-concentration. The remaining 19 targeted metabolites were either at, or below, the limit of detection. The current approach provides a good workflow for absolute quantification of intermediates in C(1)-carbon metabolism in natural microbial communities.     

Direct measurement of isotopomer of intracellular metabolites using capillary electrophoresis time-of-flight mass spectrometry for efficient metabolic flux analysis

We have developed a metabolic flux analysis method that is based on (13)C-labeling patterns of the intracellular metabolites directly measured by capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS). The flux distribution of the central carbon metabolism in Escherichia coli was determined by this new approach and the results were compared with findings obtained by conventional GC-MS analysis based on isotopomer of the proteinogenic amino acids. There were some differences in estimation results between new approach using CE-TOFMS and conventional approach using GC-MS. These were thought to be attributable to variations in measured mass distributions between amino acids and the corresponding precursors and to differences in the sensitivity of the exchange coefficients to mass distributions. However, our CE-TOFMS method facilitates high-throughput flux analysis without requiring complicated sample preparation such as hydrolysis of proteins and derivatization of amino acids.