Identification of wheat varieties using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry and an artificial neural network

A novel tool for variety identification of wheat (Triticum aestivum L.) has been developed: an artificial neural network (ANN) is used to classify the gliadin fraction analysed by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOFMS). The robustness of this novel method with respect to various experimental parameters has been tested. The results can be summarised: (i) With this approach 97% of the wheat varieties can be classified correctly with a corresponding correlation coefficient of 1.0, (ii) The method is fast since the time of extracting gliadins from flour can be reduced to 20 min without significant decrease in overall performance, (iii) The storage of flour or extracts under standard conditions does not influence the classification ability (i. e. the generalisation ability) of the method, and (iv) The classification obtained is not influenced by the identity of the operator making the analysis. This study demonstrates that a combination of an ANN and MALDI-TOFMS analysis of the gliadin fraction provides a fast and reliable tool for the variety identification of wheat. Copyright 1999 John Wiley & Sons, Ltd.     

Multivariate analysis of 2-DE protein patterns--practical approaches

Practical approaches to the use of multivariate data analysis of 2-DE protein patterns are demonstrated by three independent strategies for the image analysis and the multivariate analysis on the same set of 2-DE data. Four wheat varieties were selected on the basis of their baking quality. Two of the varieties were of strong baking quality and hard wheat kernel and two were of weak baking quality and soft kernel. Gliadins at different stages of grain development were analyzed by the application of multivariate data analysis on images of 2-DEs. Patterns related to the wheat varieties, harvest times and quality were detected on images of 2-DE protein patterns for all the three strategies. The use of the multivariate methods was evaluated in the alignment and matching procedures of 2-DE gels. All the three strategies were able to discriminate the samples according to quality, harvest time and variety, although different subsets of protein spots were selected. The explorative approach of using multivariate data analysis and variable selection in the analyses of 2-DEs seems to be promising as a fast, reliable and convenient way of screening and transforming many gel images into spot quantities.     

Mass spectrometry and partial least-squares regression: a tool for identification of wheat variety and end-use quality

Rapid methods for the identification of wheat varieties and their end-use quality have been developed. The methods combine the analysis of wheat protein extracts by mass spectrometry with partial least-squares regression in order to predict the variety or end-use quality of unknown wheat samples. The whole process takes approximately 30 min. Extracts of alcohol-soluble storage proteins (gliadins) from wheat were analysed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Partial least-squares regression was subsequently applied using these mass spectra for making models that could predict the wheat variety or end-use quality. Previously, an artificial neural network was used to identify wheat varieties based on their protein mass spectra profiles. The present study showed that partial least-squares regression is at least as useful as neural networks for this identification. Furthermore, it was demonstrated that partial least-squares regression could be used to predict wheat end-use quality, which has not been possible using neural networks.     

Comparison of four extraction/methylation analytical methods to measure fatty acid composition by gas chromatography in meat

Four different extraction-derivatization methods commonly used for fatty acid analysis in meat (in situ or one-step method, saponification method, classic method and a combination of classic extraction and saponification derivatization) were tested. The in situ method had low recovery and variation. The saponification method showed the best balance between recovery, precision, repeatability and reproducibility. The classic method had high recovery and acceptable variation values, except for the polyunsaturated fatty acids, showing higher variation than the former methods. The combination of extraction and methylation steps had great recovery values, but the precision, repeatability and reproducibility were not acceptable. Therefore the saponification method would be more convenient for polyunsaturated fatty acid analysis, whereas the in situ method would be an alternative for fast analysis. However the classic method would be the method of choice for the determination of the different lipid classes.     

Identification of barley and rye varieties using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry with neural networks

Cereal varieties are normally identified using time-consuming methods such as visual examination of either the intact grain or one-dimensional electrophoretic patterns of the grain storage proteins. A fast method for identification of wheat (Triticum aestivum L.) varieties has previously been developed, which combines analysis of alcohol-soluble wheat proteins (gliadins) using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry with neural networks. Here we have applied the same method for the identification of both barley (Hordeum vulgare L.) and rye (Secale cereale L.) varieties. For barley, 95% of the mass spectra were correctly classified. This is an encouraging result, since in earlier experiments only a grouping into subsets of varieties was possible. However, the method was not useful in the classification of rye, due to the strong similarity between mass spectra of different varieties.     

High-efficiency protein extraction from polyacrylamide gels for molecular mass measurement by matrix-assisted laser desorption/ionization-time of flight-mass spectrometry

A simple and fast method of protein extraction from Coomassie Brilliant Blue (CBB)-stained polyacrylamide gels suited for molecular mass measurement of proteins by matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) is reported. Proteins in CBB-stained gel pieces were extracted by a 10-min soaking in 0.1 M NaOH at 25 degrees C. The recovery of this one-step extraction method was 34-73% for proteins <67 kDa. CBB adduction to proteins during mass spectrometric analysis was avoided by a destaining step before the alkaline extraction. The molecular mass values of the extracted proteins coincided with those of purified proteins within +/-0.01-0.10% deviation for all the proteins <36 kDa. Because of the high extraction recovery, mass measurement was possible for the proteins extracted from CBB-stained gels with loaded protein quantities as little as 34 ng for cytochrome c, alpha-lactalbumin, myoglobin, beta-lactoglobulin, trypsinogen, and carbonic anhydrase (12.4-29.0 kDa), 340 ng for glyceraldehyde-3-phosphate dehydrogenase (35.6 kDa) and albumin (66.3 kDa). This method provides a highly efficient approach to utilize CBB-stained one- or two-dimensional gels for whole protein analysis using MALDI-TOF-MS.     

MALDI‐TOF mass spectrometry of hordeins: rapid approach for identification of malting barley varieties

A procedure for identification of malting barley varieties using matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) of ethanol‐soluble barley proteins (hordeins) is described. The hordeins were first extracted from milled barley grains by several extraction protocols (using different extraction agents and conditions). Hordein extracts were then analyzed directly via MALDI‐TOF MS without any preliminary purification or separation step, and the protein profiles of analyzed hordein extracts were compared in order to find out the most suitable extraction procedure for mass spectrometric analysis. The optimized procedure was successfully applied to identification of 13 malting barley varieties. Our results revealed that the proposed mass spectrometry‐based approach provides characteristic mass patterns of extracted hordeins, which can be advantageously used for barley variety identification. Copyright © 2009 John Wiley & Sons, Ltd.     

Classification of wheat varieties: use of two-dimensional gel electrophoresis for varieties that can not be classified by matrix assisted laser desorpiton/ionization-time of flight-mass spectrometry and an artificial neural network

Analyzing a gliadin extract by matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) combined with an artificial neural network (ANN) is a suitable method for identification of wheat varieties. However, the ANN can not distinguish between all different wheat varieties. Two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) was applied to three pairs of wheat varieties, which can not be classified correctly by ANN. By 2-D PAGE the varieties in the three pairs can be discriminated and these six wheat varieties can be separated from each other, which could not be separated by MALDI-TOF-MS and NN.     

Proteomic‐based analytical approach for the characterization of glutenin subunits in durum wheat

One of the main objectives of wheat glutenin subunit (GS) analysis is the identification of protein components linked to wheat quality. The proteomic characterization of glutenin has to consider the relatively low levels of arginine and lysine residues and the close sequence similarity among the different groups of these subunits, which hinders or even prevents the identification of the GS. In this study, a proteomic approach has been applied to resolve the heterogeneity of wheat glutenin components. Proteins extracted from Triticum durum flour were first analyzed by two‐dimensional gel electrophoresis, which greatly reduced glutenin complexity. The identity of each spot was confirmed by nano liquid chromatography tandem mass spectrometry analysis of tryptic peptides. In parallel, measurements of the high mass range by matrix‐assisted laser desorption/ionization time‐of‐flight analysis allowed detection of the large tryptic peptides. Gathering all data from search engine interrogation, very high sequence coverage was obtained for high molecular weight GS, including Bx7 and By8, in agreement with the known genetic profile of durum wheat. In addition, a truncated form of By8, never detected before, was also found. Low molecular weight GS (LMW‐GS) B‐type was identified with reasonable sequence coverage, while a clear identification of LWM‐GS C‐ and D‐type was hindered by the incompleteness of the wheat DNA databases. This study represents the first comprehensive analysis of the glutenin proteome and provides a reliable method for classifying wheat varieties according to their glutenin profile. Copyright © 2009 John Wiley & Sons, Ltd.     

A generic fast solid-phase extraction high-performance liquid chromatography/mass spectrometry method for high-throughput drug discovery

High-performance liquid chromatography/mass spectrometry (HPLC/MS) is increasingly perceived to be an essential tool in drug discovery at many key steps, like drug screening, lead identification, ADME profiling, and drug metabolism and pharmacology studies. High-throughput screenings in the early phase for metabolic stability, protein binding, permeability (ADME) and bioavailability are widely used to weed out compounds that do not exhibit the necessary characteristics. For such high-throughput LC/MS studies, a generic LC/MS method that can be used for a variety of compounds is desired. In this study, we used a small set of compounds with a wide range of properties to guide method development, and achieved a sample throughput of 1.7 min/sample. Here, we present a generic fast method that achieves good peak separation and peak shape on conventional HPLC systems using a column-switching mechanism for on-line solid-phase extraction (SPE)-HPLC/MS analysis. The method has a linear response range from 1 to 500 nM for the tested compounds. When a larger set of 658 randomly picked small molecules were analyzed using this method, 612 were observed with good signal intensity and HPLC peak shapes. This generic fast SPE-LC/MS method has been used to screen more than 1.5 million compounds repetitively against over 200 protein targets for hit confirmation and semi-quantitation of binding constants from biological assays. Over 7000 different compounds for a variety of protein-binding assays have been studied using this method for quantitative analysis as well.     

Simple Methodology for the Quantitative Analysis of Fatty Acids in Human Red Blood Cells

In the last years, there has been an increasing interest in evaluating possible relations between fatty acid (FA) patterns and the risk for chronic diseases. Due to the long life span (120 days) of red blood cells (RBCs), their FA profile reflects a longer term dietary intake and was recently suggested to be used as an appropriate biomarker to investigate correlations between FA metabolism and diseases. Therefore, the aim of this work was to develop and validate a simple and fast methodology for the quantification of a broad range of FAs in RBCs using gas chromatography with flame ionization detector, as a more common and affordable equipment suitable for biomedical and nutritional studies including a large number of samples. For this purpose, different sample preparation protocols were tested and compared, including a classic two-step method (Folch method) with modifications and different one-step methods, in which lipid extraction and derivatization were performed simultaneously. For the one-step methods, different methylation periods and the inclusion of a saponification reaction were evaluated. Differences in absolute FA concentrations were observed among the tested methods, in particular for some metabolically relevant FAs such as trans elaidic acid and eicosapentaenoic acid. The one-step method with saponification and 60 min of methylation time was selected since it allowed the identification of a higher number of FAs, and was further submitted to in-house validation. The proposed methodology provides a simple, fast and accurate tool to quantitatively analyse FAs in human RBCs, useful for clinical and nutritional studies.     

Simple Methodology for the Quantitative Analysis of Fatty Acids in Human Red Blood Cells

In the last years, there has been an increasing interest in evaluating possible relations between fatty acid (FA) patterns and the risk for chronic diseases. Due to the long life span (120 days) of red blood cells (RBCs), their FA profile reflects a longer term dietary intake and was recently suggested to be used as an appropriate biomarker to investigate correlations between FA metabolism and diseases. Therefore, the aim of this work was to develop and validate a simple and fast methodology for the quantification of a broad range of FAs in RBCs using gas chromatography with flame ionization detector, as a more common and affordable equipment suitable for biomedical and nutritional studies including a large number of samples. For this purpose, different sample preparation protocols were tested and compared, including a classic two-step method (Folch method) with modifications and different one-step methods, in which lipid extraction and derivatization were performed simultaneously. For the one-step methods, different methylation periods and the inclusion of a saponification reaction were evaluated. Differences in absolute FA concentrations were observed among the tested methods, in particular for some metabolically relevant FAs such as trans elaidic acid and eicosapentaenoic acid. The one-step method with saponification and 60 min of methylation time was selected since it allowed the identification of a higher number of FAs, and was further submitted to in-house validation. The proposed methodology provides a simple, fast and accurate tool to quantitatively analyse FAs in human RBCs, useful for clinical and nutritional studies.

     

Fast and efficient extraction methods for the analysis of polychlorinated biphenyls and polybrominated diphenyl ethers in biological matrices

This paper describes fast and simple extraction methods for the determination of polychlorinated biphenyls and polybrominated diphenyl ethers in biological matrices. Four extraction protocols were tested. The first protocol used microwave-assisted extraction combined with two purification steps. The second one was similar, except that microwave-assisted extraction was replaced by accelerated solvent extraction. The third one combined extraction/purification by accelerated solvent extraction with final purification on a silica gel column. The last one combined microwave-assisted extraction with purification on an acidic silica gel column. The protocols were tested on various matrices: a spiked matrix, two certified matrices (SRM 2977, WMF 01), and natural matrices (mysids and fish). All of the protocols produced good performance in terms of recovery and reproducibility. The two last protocols showed promising results in terms of applicability to natural matrices, as they required a minimum of sample handling and minimal amounts of solvent and time. These methods allowed at least 24 samples to be handled per day, and could easily be used for routine analysis. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A rapid (less than 10 minute) electrophoresis method for identification of wheat varieties

Conventional procedures for electrophoretic identification of grain samples according to variety are too slow to permit checking at the time of delivery. The method described permits electrophoretic identification within an hour. It involves extraction of gliadin proteins from crushed grain with 6% urea solution or ethylene glycol, cathodic electrophoresis for 9 min at 300 V in a Micrograd gel (MG 315 from Gradipore Ltd, Sydney, Australia) using sodium lactate buffer (pH 3.1), and staining in Gradipore (at about 50 degrees C). Distinction between a set of Australian varieties was similar to that obtainable with the Australian Standard Procedure.     

HPLC and GC-MS determination of bioactive compounds in microwave obtained extracts of three varieties of Labisia pumila Benth

Microwave extraction of phytochemicals from medicinal plant materials has generated tremendous research interest and shown great potential. This research highlights the importance of microwave extraction in the analysis of flavonoids, isoflavonoid and phenolics and the antioxidant properties of extracts from three varieties of the Malaysian medicinal herb, Labisia pumila Benth. High and fast extraction performance ability, equal or higher extraction efficiencies than other methods, and the need for small samples and reagent volumes are some of the attractive features of this new promising microwave assisted extraction (MAE) technique. The aims of the present research were to determine the foliar phenolics and flavonoids contents of extracts of three varieties of L. pumila obtained by a microwave extraction method while flavonoid, isoflavonoid and phenolic compounds were analyzed using RP-HPLC. Furthermore, the antioxidant activities were measured by the DPPH and FRAP methods and finally, the chemical composition of the crude methanolic extracts of the leaves of all three varieties were analyzed by GS-MS.     

Solid-phase microextraction of hop volatiles. Potential use for determination and verification of hop varieties

The composition of hop essential oil is an important tool for evaluation of hop quality. As each hop variety has a typical essential oil pattern (fingerprint), hop oil analyses can be used to distinguish between hop varieties. The headspace solid-phase microextraction (SPME) method as described in this contribution is a simple sample preparation technique and represents an alternative procedure for essential oil fingerprint determination. Different SPME parameters (extraction temperature, extraction time and sample mass) were studied and the results were compared with those obtained by the routine distillation method. It is shown that SPME results can be used for determination and verification of varieties grown in Slovenia by means of principal components analysis.     

Application of multiwalled carbon nanotubes for solid-phase extraction of organophosphate pesticide

Multiwalled carbon nanotube (MWCNT) was developed as a new sorbent for solid-phase extraction (SPE) of organophosphate (OP) pesticides. A combination of SPE with square-wave voltammetric (SWV) analysis resulted in a fast, sensitive, and selective electrochemical method for determination of OP pesticide using methyl parathion (MP) as a representative. Because of the strong affinity of MWCNT for phosphoric group, nitroaromatic OP compounds can strongly bind to the MWCNT surface. The macroporosity and heterogeneity of MWCNT allow extracting a large amount of MP less than 5 min. The stripping response was highly linear over the MP range of 0.05–2.0 μg/mL, with a detection limit of 0.005 μg/mL. The determination of MP in garlic samples showed acceptable accuracy. The fast extraction ability of MWCNT makes it promising sorbent for various solid-phase extractions.     

石蜡包埋组织中组蛋白的提取分离和翻译后修饰的定量分析

组蛋白翻译后修饰(HPTMs)参与基因转录调控,其异常与肿瘤等重大疾病的发生发展密切相关。石蜡包埋组织是当前疾病研究的重要样本资源,对肿瘤机制和标志物研究具有重要意义。目前基于质谱的蛋白质组学技术已成为HPTMs分析的有力工具,而针对福尔马林固定石蜡包埋(FFPE)组织样品的HPTMs分析还十分有限。该研究发展了一种基于高效液相色谱-串联质谱的FFPE组织样本HPTMs分离分析新方法。通过研究并优化组蛋白的提取策略,建立了FFPE组织样本脱蜡水化处理、蛋白质提取与聚丙烯酰胺凝胶电泳分离相结合的组蛋白提取和分离方法。通过研究FFPE切片数量、组蛋白化学衍生化方法等对组蛋白鉴定的影响,确定了组蛋白处理的具体步骤。通过HPLC分离结合非依赖性采集模式的质谱分析,鉴定了组蛋白修饰的类型、位点和丰度。最后,将优化的实验方法应用于FFPE临床样本的HPTMs分析,鉴定了2例人乳腺浸润性癌和癌旁正常组织的HPTMs图谱,均获得了100种以上的不同组蛋白修饰形式的多肽。定量分析了他们的差异性水平,通过主成分降维分析,发现浸润性癌和癌旁正常组织之间组蛋白修饰丰度存在明显的差异,且差异性具有一定的规律,特别是涉及转录调控的组蛋白修饰与乳腺癌的预后和治疗靶点具有相关性,进而探讨了乳腺癌中异常HPTMs的生物学意义。该研究对临床石蜡样本中组蛋白修饰的分离分析以及肿瘤表观遗传标志物的检测进行了有益的探索。     

Comprehensive evaluation of solvent in dispersive liquid-liquid microextraction for determination of itraconazole and hydroxy itraconazole by high performance liquid chromatography with fluorescence detection

This paper aims to propose a multicriteria decision analysis (MCDA) method to evaluate and select solvent in a dispersive liquid-liquid microextraction (DLLME) approach. The DLLME is applied to the determination of itraconazole and hydroxy itraconazole in plasma by high performance liquid chromatography with fluorescence detection (HPLC-FLD). To achieve this goal, extraction efficiency, chromatographic resolution, and greenness of solvent were identified as the three indicators in MCDA. Then, Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) was employed to evaluate and select the solvent. Weight assignment was set up by integrating the subjective scoring from experienced analysts and the objective approach using Shannon’s entropy weight method. Under chosen parameters (extraction solvent: 1-decanol 40 μL, dispersing solvent: methanol 400 μL), the method was validated satisfactorily and applied successfully to the analysis of itraconazole and hydroxy itraconazole in real human plasma samples. The results show that the comprehensive weighted TOPSIS analysis is a promising tool to choose experimental conditions toward an integrative goal. It can provide analysts with a decision making reference to maintain a balance between the analytical performance and eco-friendliness.     

Facile synthesis of a novel magnetic covalent organic frameworks for extraction and determination of five fungicides in Chinese herbal medicines

A novel magnetic covalent organic framework was synthesized via a one-step coating approach with solvothermal reaction employing 2,4,6-tris(4-aminophen-yl)-1,3,5-triazine and 2,4,6-triformylphloroglucinol as two building blocks by covalent bonding. The prepared magnetic covalent organic frameworks were properly characterized by different techniques and employed as adsorbents of magnetic solid-phase extraction. An analytical method was developed for the simultaneous determination of five fungicides in two Chinese herbal medicine samples via magnetic solid-phase extraction coupled to ultra high performance liquid chromatography with tandem mass spectrometry analysis. Under optimized magnetic solid-phase extraction conditions, the method exhibited satisfactory recoveries (74.0−109.6%) with relative standard deviations of 0.4−4.6%, low limits of detection (0.003−0.015 μg/kg), and good linearity (R² > 0.9960). Compared with the traditional extraction method, the proposed method required a lower amount of adsorbent (3 mg) and extraction time (5 min). The adsorbent also had favorable reusability (not less than eight times). Therefore, the magnetic covalent organic frameworks could be a promising adsorbent for the extraction and quantitation of fungicides in Chinese herbal medicines.