Feature selection of gas chromatography/mass spectrometry chemical profiles of basil plants using a bootstrapped fuzzy rule-building expert system

A bootstrapped fuzzy rule-building expert system (FuRES) and a bootstrapped t-statistical weight feature selection method were individually used to select informative features from gas chromatography/mass spectrometry (GC/MS) chemical profiles of basil plants cultivated by organic and conventional farming practices. Feature subsets were selected from two-way GC/MS data objects, total ion chromatograms, and total mass spectra, separately. Four economic classifiers based on the bootstrapped FuRES approach, i.e., fuzzy optimal associative memory (e-FOAM), e-FuRES, partial least-squares–discriminant analysis (e-PLS-DA), and soft independent modeling by class analogy (e-SIMCA), and four economic classifiers based on the bootstrapped t-weight approach, i.e., e-PLS-DA-t, e-FOAM-t, e-FuRES-t, and e-SIMCA-t, were constructed thereafter to be compared with full-size classifiers obtained from the entire GC/MS data objects (i.e., FOAM, FuRES, PLS-DA, and SIMCA). By using three features selected from two-way data objects, the average classification rates with e-FOAM, e-FuRES, e-PLS-DA, and e-SIMCA were 95.3?±?0.5 %, 100 %, 100 %, and 91.8?±?0.2 %, respectively. The established economic classifiers were used to classify a new validation set collected 2.5 months later with no parametric change to experimental procedure. Classification rates with e-FOAM, e-FuRES, e-PLS-DA, and e-SIMCA were 96.7 %, 100 %, 100 %, and 96.7 %, respectively. Characteristic components in basil extracts corresponding to highest-ranked useful features were putatively identified. The feature subset may prove valuable as a rapid approach for organic basil authentication.     

Screening of adulteration in packaging biocomposites by infrared spectroscopy and chemometrics

Fourier transform infrared spectroscopy coupled with chemometrics was employed to detect packaging polylactic acid-based biocomposite samples adulterated with polypropylene (PP) 30–45% and linear low-density polyethylene 2–10%. Principal component analysis, soft independent modeling of class analogy (SIMCA) and partial least square discriminate analysis (PLS-DA) chemometric techniques were utilized to classify samples in different classes. Totally, 362 samples were modeled in three different classes (two adulterated and one non-adulterated). The obtained results revealed that PLS-DA is the most suitable chemometric approach for prediction of probable adulteration in biocomposite samples with reliable specificity and selectivity. It could provide 99% correct class prediction rate between non-adulterated biocomposite samples and adulterated ones, while SIMCA methods provided 73.33% prediction accuracy in classification.     

Discrimination among Panax species using spectral fingerprinting

Spectral fingerprints of samples of three Panax species (P. quinquefolius L., P. ginseng, and P. notoginseng) were acquired using UV, near-infrared (NIR), and MS. With principal component analysis, all three methods allowed visual discrimination among the three species. All three methods were able to discriminate between white and red ginseng, and showed distinctive subgroupings of red ginseng related to root quality (age/size). Analysis of variance was used to evaluate the relative variance arising from the species, run, and analytical uncertainty, and was used to identify the most information-rich portions of the spectrum for NIR and UV. Accurate classification of the three species was obtained by using partial least squares-discriminant analysis and a fuzzy rule-building expert system. Relatively poor accuracy was obtained using soft independent modeling of class analogy when a single component was used.     

Classification of Brazilian Coffee Using Near-Infrared Spectroscopy and Multivariate Calibration

This work describes the use of near infrared spectroscopy (NIRS) and chemometric techniques calibration for the classification of coffee samples from different lots and producers acquired in supermarkets and roasting industries in some Brazilian cities. Seventy-three samples of finely ground roasted coffee were acquired in the market and 91 samples of roasted ground Arabica beans were analyzed in the full NIR spectral range (800–2500 nm) using a diffuse reflectance accessory coupled to an MB160 Bomem spectrophotometer. Two classification models were constructed: Soft Independent Modeling Class Analogy (SIMCA) and PLS Discriminant Analysis (PLS-DA). All findings reveal that NIR spectroscopy, coupled with either SIMCA or PLS-DA multivariate models, can be a useful tool to differentiate roasted coffee grains and to replace sensory tests.     

Determining the adulteration of spices with Sudan I-II-II-IV dyes by UV-visible spectroscopy and multivariate classification techniques

We propose a very simple and fast method for detecting Sudan dyes (I, II, III and IV) in commercial spices, based on characterizing samples through their UV-visible spectra and using multivariate classification techniques to establish classification rules. We applied three classification techniques: K-Nearest Neighbour (KNN), Soft Independent Modelling of Class Analogy (SIMCA) and Partial Least Squares Discriminant Analysis (PLS-DA). A total of 27 commercial spice samples (turmeric, curry, hot paprika and mild paprika) were analysed by chromatography (HPLC-DAD) to check that they were free of Sudan dyes. These samples were then spiked with Sudan dyes (I, II, III and IV) up to a concentration of 5 mg L⁻¹. Our final data set consisted of 135 samples distributed in five classes: samples without Sudan dyes, samples spiked with Sudan I, samples spiked with Sudan II, samples spiked with Sudan III and samples spiked with Sudan IV.Classification results were good and satisfactory using the classification techniques mentioned above: 99.3%, 96.3% and 90.4% of correct classification with PLS-DA, KNN and SIMCA, respectively. It should be pointed out that with SIMCA, there are no real classification errors as no samples were assigned to the wrong class: they were just not assigned to any of the pre-defined classes.     

Classification of jet fuels by fuzzy rule-building expert systems applied to three-way data by fast gas chromatography--fast scanning quadrupole ion trap mass spectrometry

A fast method that can be used to classify unknown jet fuel types or detect possible property changes in jet fuel physical properties is of paramount interest to national defense and the airline industries. While fast gas chromatography (GC) has been used with conventional mass spectrometry (MS) to study jet fuels, fast GC was combined with fast scanning MS and used to classify jet fuels into lot numbers or origin for the first time by using fuzzy rule-building expert system (FuRES) classifiers. In the process of building classifiers, the data were pretreated with and without wavelet transformation and evaluated with respect to performance. Principal component transformation was used to compress the two-way data images prior to classification. Jet fuel samples were successfully classified with 99.8 ± 0.5% accuracy for both with and without wavelet compression. Ten bootstrapped Latin partitions were used to validate the generalized prediction accuracy. Optimized partial least squares (o-PLS) regression results were used as positively biased references for comparing the FuRES prediction results. The prediction results for the jet fuel samples obtained with these two methods were compared statistically. The projected difference resolution (PDR) method was also used to evaluate the fast GC and fast MS data. Two batches of aliquots of ten new samples were prepared and run independently 4 days apart to evaluate the robustness of the method. The only change in classification parameters was the use of polynomial retention time alignment to correct for drift that occurred during the 4-day span of the two collections. FuRES achieved perfect classifications for four models of uncompressed three-way data. This fast GC/fast MS method furnishes characteristics of high speed, accuracy, and robustness. This mode of measurement may be useful as a monitoring tool to track changes in the chemical composition of fuels that may also lead to property changes.     

The use of high performance liquid chromatography-quadrupole time-of-flight mass spectrometry coupled to advanced data mining and chemometric tools for discrimination and classification of red wines according to their variety

In this study, the potential of high performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (HPLC–QTOFMS) for metabolomic profiling of red wine samples was examined. Fifty one wines representing three varieties (Cabernet Sauvignon, Merlot, and Pinot Noir) of various geographical origins were sourced from the European and US retail market. To find compounds detected in analyzed samples, an automated compound (feature) extraction algorithm was employed for processing background subtracted single MS data. Stepwise reduction of the data dimensionality was followed by principal component analysis (PCA) and partial least square-discriminant analysis (PLS-DA) which were employed to explore the structure of the data and construct classification models. The validated PLS-DA model based on data recorded in positive ionization mode enabled correct classification of 96% of samples. Determination of molecular formula and tentative identification of marker compound was carried out using accurate mass measurement of full single MS spectra. Additional information was obtained by correlating the fragments obtained by MS/MS accurate mass spectra using the QTOF with collision induced dissociation (CID) of precursor ions.     

Tracing the origin of extra virgin olive oils by infrared spectroscopy and chemometrics: A case study

In this paper, the potential of coupling mid- and near-infrared spectroscopic fingerprinting techniques and chemometric classification methods for the traceability of extra virgin olive oil samples from the PDO Sabina was investigated. To this purpose, two different pattern recognition algorithm representative of the discriminant (PLS-DA) and modeling (SIMCA) approach to classification were employed. Results obtained after processing the spectroscopic data by PLS-DA evidenced a rather high classification accuracy, NIR providing better predictions than MIR (as evaluated both in cross-validation and on an external test set). SIMCA confirmed these results and showed how the category models for the class Sabina can be rather sensitive and highly specific. Lastly, as samples from two harvesting years (2009 and 2010) were investigated, it was possible to evidence that the different production year can have a relevant effect on the spectroscopic fingerprint. Notwithstanding this, it was still possible to build models that are transferable from one year to another with good accuracy.     

Data-fusion for multiplatform characterization of an italian craft beer aimed at its authentication

Five different instrumental techniques: thermogravimetry, mid-infrared, near-infrared, ultra-violet and visible spectroscopies, have been used to characterize a high quality beer (Reale) from an Italian craft brewery (Birra del Borgo) and to differentiate it from other competing and lower quality products. Chemometric classification models were built on the separate blocks using soft independent modeling of class analogies (SIMCA) and partial least squares-discriminant analysis (PLS-DA) obtaining good predictive ability on an external test set (75% or higher depending on the technique). The use of data fusion strategies – in particular, the mid-level one – to integrate the data from the different platforms allowed the correct classification of all the training and validation samples.     

基于质子转移反应-飞行时间质谱快速鉴别不同产地闽北水仙茶

采用质子转移反应-飞行时间质谱仪(PTR-TOF-MS), 构建了3个产地(武夷山、建阳、建瓯)113个闽北水仙茶样品香气的化学指纹图谱, 对所得的闽北水仙茶香气指纹图谱进行主成分分析(PCA), 获得了不同产地闽北水仙茶样品的质谱信息特征, 然后采用软独立建模分类法(SIMCA)、K最邻近结点算法(KNN)、偏最小二乘判别分析法(PLS-DA)对闽北水仙茶的质谱信息进行了模式识别.结果表明, PTR-TOF-MS结合分类识别模式能有效区分不同产地的闽北水仙茶.PCA 提取了3个主成分, 累计贡献率为84.66%;3个识别模型的校正集判别正确率分别为89.38%、100.00%和100.00%, 预测集的判别正确率分别为83.18%、 96.46%和95.57%.基于此成功建立了不同产地的闽北水仙茶识别模型.本方法无需样品预处理、分析速度快、灵敏度高、对茶叶无损伤, 为茶叶产地溯源提供了新方法.     

Analysis of sexual assault evidence: statistical classification of condoms by ambient mass spectrometry

Desorption electrospray ionization mass spectrometry (DESI‐MS) and easy ambient sonic‐spray ionization mass spectrometry (EASI‐MS) are employed here in the forensic analysis of chemical compounds found in condoms and relative traces, and their analytical performances are compared. Statistical analysis of data obtained from mass spectra only was applied in order to obtain classification rules for distinguishing ten types of condoms. In particular, two supervised chemometric techniques [linear discriminant analysis (LDA) and soft independent modeling of class analogy (SIMCA)] were carried out on absolute and relative intensity values to test the performances of statistical models in terms of predictive capacity. The achieved classification of samples was excellent because of the high prediction percentages of the method used both for DESI and EASI mass spectrometry analyses, confirming these two as potential ambient ionization techniques for forensic analyses in case of sexual assault crimes. EASI‐MS showed 99% prediction ability for LDA using relative data and 100% prediction ability for SIMCA using both absolute and relative ones, while DESI showed 94% prediction ability for both LDA and SIMCA. The absence of any sample preparation technique gives advantages in terms of sample preservation and reduced contamination, allowing successive analyses to be performed on the same sample by other techniques. Copyright © 2015 John Wiley & Sons, Ltd.     

Preliminary study on application of mid infrared spectroscopy for the evaluation of the virgin olive oil "freshness"

The freshness of virgin olive oils (VOO) from typical cultivars of Garda regions was evaluated by attenuated total reflectance (ATR) and Fourier transform infrared (FTIR) spectroscopy, in combination with multivariate analysis. The olive oil freshness decreased during storage mainly because of oxidation processes. In this research, 91 virgin olive oils were packaged in glass bottles and stored either in the light or in the dark at room temperature for different periods. The oils were analysed, before and after storage, using both chemical methods and spectroscopic technique.Classification strategies investigated were partial least square discriminant analysis (PLS-DA), linear discriminant analysis (LDA), and soft independent modelling of class analogy (SIMCA).The results show that ATR-MIR spectroscopy is an interesting technique compared with traditional chemical index in classifying olive oil samples stored in different conditions. In fact, the FTIR PCA results allowed a better discrimination among fresh and oxidized oils, than samples separation obtained by PCA applied to chemical data. Moreover, the results obtained by the different classification techniques (PLS-DA, LDA, SIMCA) evidenced the ability of FTIR spectra to evaluate the olive oil freshness. FTIR spectroscopy results are in agreement with classical methods. The spectroscopic technique could be applied for the prediction of VOOs freshness giving information related to chemical modifications. The great advantages of this technique, compared to chemical analysis, are related to rapidity, non-destructive characteristics and low cost per sample. In conclusion, ATR-MIR represents a reliable, cheap and fast classification tool able to assess the freshness of virgin olive oils.     

Comparison of PLS1-DA, PLS2-DA and SIMCA for classification by origin of crude petroleum oils by MIR and virgin olive oils by NIR for different spectral regions

This study compares results obtained with several chemometric methods: SIMCA, PLS2-DA, PLS2-DA with SIMCA, and PLS1-DA in two infrared spectroscopic applications. The results were optimized by selecting spectral ranges containing discriminant information. In the first application, mid-infrared spectra of crude petroleum oils were classified according to their geographical origins. In the second application, near-infrared spectra of French virgin olive oils were classified in five registered designations of origins (RDOs). The PLS-DA discrimination was better than SIMCA in classification performance for both applications. In both cases, the PLS1-DA classifications give 100% good results. The encountered difficulties with SIMCA analyses were explained by the criteria of spectral variance. As a matter of fact, when the ratio between inter-spectral variance and intra-spectral variance was close to the F_c (Fisher criterion) threshold, SIMCA analysis gave poor results. The discrimination power of the variable range selection procedure was estimated from the number of correctly classified samples.     

正交信号校正在正常成人血清1H NMR谱的代谢组分析中的滤噪作用评价

观察、比较正交信号校正(OSC)滤噪前后, 用不同的模式识别方法对正常成人血清代谢组¹H NMR谱进行分析的效果, 以探讨NMR代谢组学技术应用于临床研究和疾病早期诊断的可行性. 78例正常成人在采血前按常规要求禁食8 h, 记录血清一维600 MHz氢谱后, 分别采用主成分分析(PCA)、偏最小二乘法-判别分析(PLS-DA)以及簇类的独立软模式法(SIMCA)对氢谱进行模式识别分析. 结果表明: 虽然采血前并无其它诸如饮食、生活方式、生理周期等方面的严格限制, 采用OSC 滤噪后, PLS-DA能够完全区分不同性别的血清氢谱, 其判别能力优于PCA和SIMCA. 而且采用OSC滤噪与文献报道的未经OSC处理的PLS-DA法获得的与性别分类有关的主要NMR积分区段基本相同. 从OSC去除不同数目的隐变量后所致的PLS-DA模型的性能改变可见: OSC去除两个隐变量时, 前两个隐变量的特征值明显比后面的大; 剩余残差为20.82%, 即去除了79.18%的X变量中与反应变量Y不相关的系统变异. 此时PLS-DA计算所得的隐变量个数为1; 而不使用OSC或用OSC去除一个隐变量时, PLS-DA所得的隐变量个数分别为3和2. 作为PLS-DA模型质量的评价指标, R2X表示PLS-DA模型计算所获得的隐变量反映自变量X的变异的百分比, R2Y则表示隐变量反映因变量Y的变异的百分比, Q2 (cum)为交叉验证后PLS-DA模型所获隐变量能够预测X和Y变异的累计百分比. R2X在OSC去除两个隐变量时达到最低值, 表明此时PLS-DA计算模型包含的系统变异最少; R2Y与Q2 (cum)都达到80%以上并趋于稳定, 说明OSC去除两个隐变量时PLS-DA模型的质量优良. 显然, OSC可去除饮食、环境等因素的影响, 降低临床样本的不均一性, 这对于NMR代谢组学技术应用于临床研究至关重要. OSC滤噪去除的隐变量个数应根据剩余残差、去除隐变量的特征值大小、PLS-DA模型计算所得的隐变量个数和反映模型质量的相关指标加以判断.     

Paper spray mass spectrometry and PLS-DA improved by variable selection for the forensic discrimination of beers

Paper spray mass spectrometry (PS-MS) combined with partial least squares discriminant analysis (PLS-DA) was applied for the first time in a forensic context to a fast and effective differentiation of beers. Eight different brands of American standard lager beers produced by four different breweries (141 samples from 55 batches) were studied with the aim at performing a differentiation according to their market prices. The three leader brands in the Brazilian beer market, which have been subject to fraud, were modeled as the higher-price class, while the five brands most used for counterfeiting were modeled as the lower-price class. Parameters affecting the paper spray ionization were examined and optimized. The best MS signal stability and intensity was obtained while using the positive ion mode, with PS(+) mass spectra characterized by intense pairs of signals corresponding to sodium and potassium adducts of malto-oligosaccharides. Discrimination was not apparent neither by using visual inspection nor principal component analysis (PCA). However, supervised classification models provided high rates of sensitivity and specificity. A PLS-DA model using full scan mass spectra were improved by variable selection with ordered predictors selection (OPS), providing 100% of reliability rate and reducing the number of variables from 1701 to 60. This model was interpreted by detecting fifteen variables as the most significant VIP (variable importance in projection) scores, which were therefore considered diagnostic ions for this type of beer counterfeit.     

Hydrophilic interaction liquid chromatography with tandem mass spectrometry for the determination of underivatized dencichine (beta-N-oxalyl-L-alpha,beta-diaminopropionic acid) in Panax medicinal plant species

Dencichine (beta-N-oxalyl-L-alpha,beta-diaminopropionic acid) is a haemostatic agent present in important Chinese medicinal herbs such as Panax notoginseng, as well as other Panax species. It is also a reported neurotoxic agent found in Lathyrus sativus (grass pea seed). A selective analytical method incorporating hydrophilic interaction chromatography with positive electrospray ionization tandem mass spectrometry (HILIC/ESI-MS/MS), for the analysis of dencichine in Panax plant species, was developed. Using multiple reaction monitoring (MRM) mode, underivatized dencichine, a small and highly polar compound, was selectively detected and quantified. The contents of dencichine in raw and steamed Panax notoginseng roots, 11 pairs of raw and steamed P. notoginseng herbal products, Panax ginseng roots, and Panax quinquefolium roots, were analyzed and compared. Optimal sensitivity of 0.3 ppm (detection limit) and 1.5 ppm (quantification limit) was achieved. The method was rapid (< or =5 min), with the HILIC peak eluting at about 1 min. Steamed P. notoginseng samples were found to contain less dencichine than the corresponding raw samples, and there were also differences among the three Panax species; raw P. ginseng and P. quinquefolium contained less dencichine than the raw P. notoginseng species. This rapid and specific method may be applied to the quantification of dencichine in complex medicinal plants and their products.     

Laser-induced breakdown spectroscopy and chemometrics for classification of toys relying on toxic elements

Quality control of toys for avoiding children exposure to potentially toxic elements is of utmost relevance and it is a common requirement in national and/or international norms for health and safety reasons. Laser-induced breakdown spectroscopy (LIBS) was recently evaluated at authors' laboratory for direct analysis of plastic toys and one of the main difficulties for the determination of Cd, Cr and Pb was the variety of mixtures and types of polymers. As most norms rely on migration (lixiviation) protocols, chemometric classification models from LIBS spectra were tested for sampling toys that present potential risk of Cd, Cr and Pb contamination. The classification models were generated from the emission spectra of 51 polymeric toys and by using Partial Least Squares - Discriminant Analysis (PLS-DA), Soft Independent Modeling of Class Analogy (SIMCA) and K-Nearest Neighbor (KNN). The classification models and validations were carried out with 40 and 11 test samples, respectively. Best results were obtained when KNN was used, with corrected predictions varying from 95% for Cd to 100% for Cr and Pb.     

The Use of UV Spectroscopy and SIMCA for the Authentication of Indonesian Honeys According to Botanical,Entomological and Geographical Origins

As a functional food, honey is a food product that is exposed to the risk of food fraud. To mitigate this, the establishment of an authentication system for honey is very important in order to protect both producers and consumers from possible economic losses. This research presents a simple analytical method for the authentication and classification of Indonesian honeys according to their botanical, entomological, and geographical origins using ultraviolet (UV) spectroscopy and SIMCA (soft independent modeling of class analogy). The spectral data of a total of 1040 samples, representing six types of Indonesian honey of different botanical, entomological, and geographical origins, were acquired using a benchtop UV-visible spectrometer (190–400 nm). Three different pre-processing algorithms were simultaneously evaluated; namely an 11-point moving average smoothing, mean normalization, and Savitzky–Golay first derivative with 11 points and second-order polynomial fitting (ordo 2), in order to improve the original spectral data. Chemometrics methods, including exploratory analysis of PCA and SIMCA classification method, was used to classify the honey samples. A clear separation of the six different Indonesian honeys, based on botanical, entomological, and geographical origins, was obtained using PCA calculated from pre-processed spectra from 250–400 nm. The SIMCA classification method provided satisfactory results in classifying honey samples according to their botanical, entomological, and geographical origins and achieved 100% accuracy, sensitivity, and specificity. Several wavelengths were identified (266, 270, 280, 290, 300, 335, and 360 nm) as the most sensitive for discriminating between the different Indonesian honey samples.     

Rapid identification and classification of Mycobacterium spp. using whole-cell protein barcodes with matrix assisted laser desorption ionization time of flight mass spectrometry in comparison with multigene phylogenetic analysis

The need of quick diagnostics and increasing number of bacterial species isolated necessitate development of a rapid and effective phenotypic identification method. Mass spectrometry (MS) profiling of whole cell proteins has potential to satisfy the requirements. The genus Mycobacterium contains more than 154 species that are taxonomically very close and require use of multiple genes including 16S rDNA for phylogenetic identification and classification. Six strains of five Mycobacterium species were selected as model bacteria in the present study because of their 16S rDNA similarity (98.4–99.8%) and the high similarity of the concatenated 16S rDNA, rpoB and hsp65 gene sequences (95.9–99.9%), requiring high identification resolution. The classification of the six strains by MALDI TOF MS protein barcodes was consistent with, but at much higher resolution than, that of the multi-locus sequence analysis of using 16S rDNA, rpoB and hsp65. The species were well differentiated using MALDI TOF MS and MALDI BioTyper™ software after quick preparation of whole-cell proteins. Several proteins were selected as diagnostic markers for species confirmation. An integration of MALDI TOF MS, MALDI BioTyper™ software and diagnostic protein fragments provides a robust phenotypic approach for bacterial identification and classification.     

Multivariate analysis of laser-induced breakdown spectroscopy chemical signatures for geomaterial classification

A large suite of natural carbonate, fluorite and silicate geological materials was studied using laser-induced breakdown spectroscopy (LIBS). Both single- and double-pulse LIBS spectra were acquired using close-contact benchtop and standoff (25 m) LIBS systems. Principal components analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were used to identify the distinguishing characteristics of the geological samples and to classify the materials. Excellent discrimination was achieved with all sample types using PLS-DA and several techniques for improving sample classification were identified. The laboratory double-pulse LIBS system did not provide any advantage for sample classification over the single-pulse LIBS system, except in the case of the soil samples. The standoff LIBS system provided comparable results to the laboratory systems. This work also demonstrates how PCA can be used to identify spectral differences between similar sample types based on minor impurities.