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Ripening is a crucial step to guarantee the high commercial value of cheddar cheese, one of the dairy products the European Union exports the most. Although several methods have lately been proposed to assess its ageing process from a chemical point of view, the majority of them is not particularly time-efficient and implies destructive analytical tests, thus, exhibiting limitations for, e.g., industrial applications. Here, a fast approach based on combining Raman and Mid-InfraRed (MIR) spectroscopy with ANOVA-Simultaneous Component Analysis (ASCA) is proposed in a low-level data fusion framework. This approach allowed to evaluate how storage temperature and time (as well as their interaction) influence cheddar ripening in a relatively cheap, rapid and green fashion.

Systemic metabolic changes after renal transplantation reflect the key processes that are related to graft accommodation. In order to describe and better understand these changes, the 1HNMR based metabolomics approach was used. The changes of 47 metabolites in the serum samples of 19 individuals were interpreted over time with respect to their levels prior to transplantation. Considering the specific repeated measures design of the experiments, data analysis was mainly focused on the multiple analyses of variance (ANOVA) methods such as ANOVA simultaneous component analysis and ANOVA-target projection. We also propose here the combined use of ANOVA and classification and regression trees (ANOVA-CART) under the assumption that a small set of metabolites the binary splits on which may better describe the graft accommodation processes over time. This assumption is very important for developing a medical protocol for evaluating a patient’s health state. The results showed that besides creatinine, which is routinely used to monitor renal activity, the changes in levels of hippurate, mannitol and alanine may be associated with the changes in renal function during the post-transplantation recovery period. Specifically, the level of hippurate (or histidine) is more sensitive to any short-term changes in renal activity than creatinine.

Data tables from experimental designs with multiple response variables and a large number of responses with respect to the number of observations are becoming more common, particularly in the omics and chemometrics fields. Traditional multivariate modelling approaches are not suitable for this type of data and more complex approaches like ANOVA Simultaneous Component Analysis (ASCA) and ANOVA Principal Component Analysis (APCA) have been developed to analyse them. They combine a matrix decomposition based on an ANOVA model with a multivariate step, Principal Component Analysis (PCA), which is applied to each decomposed matrix. This article compares ASCA and APCA to three other and less known techniques combining ANOVA and a multivariate step: PArallel Factor - Simultaneous Component Analysis (PARAFASCA), ANOVA Common Dimensions (AComDim), and ANOVA Multi-block Orthogonal Partial Least Squares (AMOPLS). The main advantages of these three methods are their ability to explore in a single and global procedure all (or a part) of the model effects, extract automatically the most important ones, interpret them visually and quantify their respective importance and significance. Theses approaches are presented in a common framework to make their comparison easier, some enhancements are introduced and they are also extended to unbalanced experimental designs thanks to a GLM version of the matrix decomposition. The three methods are applied to a 1H NMR data set with a three-factor unbalanced experimental design. Quantitative and visual results are compared for the three techniques and show that they are all suitable for the analysis of a complex model, but differ in the type of outputs and the ease of interpretation of the results. This opens perspectives for the analysis of even more complex data, including models with random or quantitative effects.

Longitudinal intervention studies with repeated measurements over time are an important type of experimental design in biomedical research. Due to the advent of “omics”-sciences (genomics, transcriptomics, proteomics, metabolomics), longitudinal studies generate increasingly multivariate outcome data. Analysis of such data must take both the longitudinal intervention structure and multivariate nature of the data into account. The ASCA+-framework combines general linear models with principal component analysis and can be used to separate and visualize the multivariate effect of different experimental factors. However, this methodology has not yet been developed for the more complex designs often found in longitudinal intervention studies, which may be unbalanced, involve randomized interventions, and have substantial missing data. Here we describe a new methodology, repeated measures ASCA+ (RM-ASCA+), and show how it can be used to model metabolic changes over time, and compare metabolic changes between groups, in both randomized and non-randomized intervention studies. Tools for both visualization and model validation are discussed. This approach can facilitate easier interpretation of data from longitudinal clinical trials with multivariate outcomes., Author summary Clinical trials are increasingly generating large amounts of complex biological data. Examples can include measuring metabolism or gene expression in tissue or blood sampled repeatedly over the course of a treatment. In such cases, one might wish to compare changes in not one, but hundreds, or thousands of variables simultaneously. In order to effectively analyze such data, both the study design and the multivariate nature of the data should be considered during data analysis. ANOVA simultaneous component analysis+ (ASCA+) is a statistical method which combines general linear models with principal component analysis, and provides a way to separate and visualize the effects of different factors on complex biological data. In this work, we describe how repeated measures linear mixed models, a class of models commonly used when analyzing changes over time and treatment effects in longitudinal studies, can be used together with ASCA+ for analyzing clinical trials in a novel method called repeated measures-ASCA+ (RM-ASCA+).

This study explores the effect of different settings on beer fermentation process applying an interval-based version of ASCA on FT-IR data. Three main factors (yeast type, temperature, fermentation time) are included in the experimental design, being high sources of variation in brewing and strictly interdependent; thus, difficult to be studied through a univariate approach. The three-factor full factorial design leads to a spectral multi-set data, with a total of 12 independent fermentations, which is explored combining ASCA and an interval adaptation of ASCA (interval-ASCA or i-ASCA). The ASCA models calculated on two separate regions (2900–2250 cm −1 and 1500–980 cm −1 ) shows differences for average time levels and the interaction between yeast types and time linked to carbon dioxide, maltose consumption and ethanol production, respectively. To better investigate the punctual influence of the studied factors on the so-called IR fingerprint region, permutation testing of ASCA in variable intervals is investigated. The analysis highlights the significant effect not only of the fermentation in all intervals considered, but also the role of other factors, such as time × yeast, yeast and temperature, in smaller variable regions. The proposed approach demonstrates how interval-ASCA on FT-IR data, isolating the variation in the data according to the experimental design used, allows a rapid and accurate test for parameter control in beer manufacturing.

When analyzing experimental chemical data, it is often necessary to incorporate the structure of the study design into the chemometric/statistical models to effectively address the research questions of interest. ANOVA-Simultaneous Component Analysis (ASCA) is one of the most prominent methods to include such information in the quantitative analysis of multivariate data, especially when the number of variables is large. This tutorial review intends to explain in a simple way how ASCA works, how it is operated and how to correctly interpret ASCA results, with approachable mathematical and visual descriptions. Two examples are given: the first, a simulated chemical reaction, serves to illustrate the ASCA steps and the second, from a real chemical ecology data set, the interpretation of results. An overview of methods closely related to ASCA is also provided, pointing out their differences and scope, to give a wide-ranging picture of the available options to build multivariate models that take experimental design into account., Graphical abstract Image 1, Highlights • ASCA is a multivariate method for analysis of multi-factor data. • An overview of the (mathematical) principles of ASCA is presented. • Key aspects for practical application of ASCA are discussed. • Detailed explanation of ASCA output in terms of score and loading plots is given. • Literature review of other multivariate techniques for analysis of multi-factor data.

Introduction Integrative analysis of multiple data sets can provide complementary information about the studied biological system. However, data fusion of multiple biological data sets can be complicated as data sets might contain different sources of variation due to underlying experimental factors. Therefore, taking the experimental design of data sets into account could be of importance in data fusion concept. Objectives In the present work, we aim to incorporate the experimental design information in the integrative analysis of multiple designed data sets. Methods Here we describe penalized exponential ANOVA simultaneous component analysis (PE-ASCA), a new method for integrative analysis of data sets from multiple compartments or analytical platforms with the same underlying experimental design. Results Using two simulated cases, the result of simultaneous component analysis (SCA), penalized exponential simultaneous component analysis (P-ESCA) and ANOVA-simultaneous component analysis (ASCA) are compared with the proposed method. Furthermore, real metabolomics data obtained from NMR analysis of two different brains tissues (hypothalamus and midbrain) from the same piglets with an underlying experimental design is investigated by PE-ASCA. Conclusions This method provides an improved understanding of the common and distinct variation in response to different experimental factors.

Chronic atrophic gastritis (CAG) is one of the most important pre-cancerous states with a high prevalence. Deciphering its mechanical network is of significant importance for its diagnosis and treatment. The time-series factor associated with CAG progression specially needs to be considered together with its biological condition. In the present work, 1H NMR-based dynamic metabonomics was firstly performed to analyze the urinary metabolic features of CAG coupled with ANOVA-simultaneous component analysis (ASCA). As results, 4 (alanine, lipids, creatine, and dimethylglycine), 2 (α-ketoglutarate and alanine) and 5 (succinate, α-ketoglutarate, alanine, hippurate, and allantoin) urine metabolites were finally selected as the candidate biomarkers related to phenotype, time, and their interaction, respectively. Mechanistically, the network pharmacology analysis further revealed these metabolites were involved into mitochondrial function, oxidation reduction, cofactor binding, generation of precursor metabolites and energy, nucleotide binging, coenzyme metabolic process, cofactor metabolic process, cellular respiration, and tricarboxylic acid cycle. Especially, mitochondria were the most important targeted organelle referred 30 targeted proteins. The present work provided a novel network pharmacology approach for elucidating the mechanisms underlying the pathogenesis of CAG based on urinary time dependent metabonomics.

Near-infrared spectroscopy (NIRS) can be a faster and more economical alternative to traditional methods for screening varietal mixtures of nursery plants during the propagation process to ensure varietal purity and to avoid errors in the dispatch batches. The global objective of this work was to develop and optimize a NIR spectral collection method for construction of robust multivariate discrimination models. Three different varieties of Prunus dulcis (Avijor, Guara, and Pentacebas) of agricultural interest were used for this study. Sources of variation were investigated, including the position of the leaves on the trees, differences among trees of the same variety, and differences at the varietal level. Three types of processed samples were investigated. Fresh leaves, dried leaves, and dried leaves in powder form were included in each analysis. A study of spectral pre-treatment methods was also performed, and multivariate methods were applied to analyze the influence of different factors on classification. These included principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), and ANOVA simultaneous component analysis (ASCA). The results indicated that variety was the most important factor for classification. The spectral pre-treatment that provided the best results was a combination of standard normal variate (SNV), Savitzky-Golay first derivative, and mean-centering methods. With regard to the type of processed sample, the highest percentages of correct classifications were obtained with fresh and dried powdered leaves at both the training set and test set validation levels. This study represents the first step towards the consolidation of NIRS as a method to identify Prunus dulcis varieties.

Basil is a plant known worldwide for its culinary and health attributes. It counts more than a hundred and fifty species and many more chemo-types due to its easy cross-breeds. Each species and each chemo-type have a typical aroma pattern and selecting the proper one is crucial for the food industry. Twelve basil varieties have been studied over three years (2018–2020), as have four different cuts. To characterize the aroma profile, nine typical basil flavour molecules have been selected using a gas chromatography–mass spectrometry coupled with an olfactometer (GC–MS/O). The concentrations of the nine selected molecules were measured by an ultra-fast CG e-nose and Principal Component Analysis (PCA) was applied to detect possible differences among the samples. The PCA results highlighted differences between harvesting years, mainly for 2018, whereas no observable clusters were found concerning varieties and cuts, probably due to the combined effects of the investigated factors. For this reason, the ANOVA Simultaneous Component Analysis (ASCA) methodology was applied on a balanced a posteriori designed dataset. All the considered factors and interactions were statistically significant (p &lt, 0.05) in explaining differences between the basil aroma profiles, with more relevant effects of variety and year.

NIR spectroscopy combined with chemometric analysis has proven to be a rapid and cost-effective screening tool for the detection of syrup-adulterated honey. Processing and storage conditions which alter the chemical and physical state of honey may affect the spectra. The effects of age, storage temperature, syrup adulteration (10 and 20% w/w) and irradiation treatment on the NIR spectra of honey were investigated as a function of time with ANOVA-simultaneous component analysis (ASCA), an experimental design-focused exploratory data analysis method. The factors 'time', 'temperature' and 'adulteration' were found to have significant effects (p 0.05), but no significant effect was observed for irradiation treatment. A significant interaction effect was found between factors 'time' and 'adulteration', with the greatest disparity between authentic and adulterated class signals found immediately after adulteration and decreasing within three months thereafter.

The application of 1H NMR spectroscopy and chemometrics for the analysis of extracts of Lantana camara is described. This approach allowed to predict the leishmanicidal activity of samples obtained at different harvest times from their 1H NMR spectra. The anti-leishmanial activity of dichloromethane extracts obtained from the aerial parts of L. camara was measured using an in vitro assay. As the extracts displayed differences in their activity according to a one-way ANOVA analysis, their 1H NMR spectra were subjected to multivariate analysis using exploratory (Principal Component Analysis (PCA) and Anova Simultaneous Component Analysis (ASCA)) and regression, (Partial Least Squares Regression to Latent Structures (PLS)) chemometrics methods. These analyses allowed to establish and characterize a predictive model capable of determining the anti-leishmanial activity of Lantana camara dichloromethane extracts from their 1H NMR spectra. Figures of merit of the developed method are given as well. The identified chemical signals responsible for the iPLS calibration model corresponded to the presence of eicosane, caryophyllene oxide, β-ionone, tiglic acid, lantanilic acid, camaric acid, and lantadene B; the chemical markers. This study proposed a fast and simple method that avoids the need of using complex biological assays to predict the leishmanicidal activity of L. camara dichloromethane extracts.

The presence of pharmaceuticals and personal care products (PPCPs) in natural water resources due to incomplete removal in Wastewater Treatment Plants (WWTPs) is a serious environmental concern at present. In this work, the effects of three pharmaceuticals (propranolol, triclosan, and nimesulide) on Gammarus pulex metabolic profiles at different doses and times of exposure have been investigated by liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS). The complex data sets generated in the different exposure experiments were analyzed with the ROIMCR procedure, based on the selection of the MS regions of interest (ROI) data and on their analysis by the Multivariate Curve-Resolution Alternating Least Squares (MCR-ALS) chemometrics method. This approach, allowed the resolution and identification of the metabolites present in the analyzed samples, as well as the estimation of their concentration changes due to the exposure experiments. ANOVA Simultaneous Component Analysis (ASCA) and Partial Least Squares Discriminant Analysis (PLS-DA) were then conducted to assess the changes in the concentration of the metabolites for the three pharmaceuticals at the different conditions of exposure. The three tested pharmaceuticals changed the concentrations of metabolites, which were related to different KEGG functional classes. These changes summarize the biochemical response of Gammarus pulex to the exposure by the three investigated pharmaceuticals. Possible pathway alterations related to protein synthesis and oxidative stress were observed in the concentration of identified metabolites., The research leading to these results has received funding from Spanish Ministerio de Ciencia e Innovación, Spain (PID2019-105732GB-C21) and Generalitat de Catalunya, Spain (project 2017-SGR-753). This work was partly supported by funding from the Biotechnology and Biological Sciences Research Council (project reference: BB/P005187/1). Funding bodies played no role in the design of the study or decision to publish. Dr. Thomas H. Miller is acknowledged for help in the sampling of Gammarus pulex from the River Cray, UK.

The dairy industry is continuously developing new strategies to obtain healthier dairy products preserving expected properties. However, when modifying a food process, the reassessment of each parameters and their interaction should be considered as highly influencing the final quality. Among others, rennet process features are fundamental for both sensory properties and typical characteristics of a cheese. In this contest, the research addresses the development of a FT-NIR spectroscopic method, coupled with chemometrics, for the study of the effect of process variables on milk renneting. The effects of temperature (30 °C, 35 °C, 40 °C), milk fat concentration (0.1, 2.55, 5 g/100 mL), and pH (6.3, 6.5, 6.7) were investigated by means of a Box-Behnken experimental design. FT-NIR data collected along the 17 trials were explored by interval-PCA (i-PCA) and ANOVA-simultaneous component analysis (ASCA). i-PCA revealed differences in the occurrence and trends of coagulation phases, related to the three considered factors. ASCA allowed the characterization of renneting evolution and the assessment of the factor role, demonstrating that main and interaction effects are significant for the process progress. The proposed approach demonstrated that i-PCA and ASCA on FT-NIR data, highlighting the effects of the operating factors, allow a rapid and accurate analysis of process modifications in cheese manufacturing.

Introduction: Modern omics experiments pertain not only to the measurement of many variables but also follow complex experimental designs where many factors are manipulated at the same time. This data can be conveniently analyzed using multivariate tools like ANOVA-simultaneous component analysis (ASCA) which allows interpretation of the variation induced by the different factors in a principal component analysis fashion. However, while in general only a subset of the measured variables may be related to the problem studied, all variables contribute to the final model and this may hamper interpretation.Objectives: We introduce here a sparse implementation of ASCA termed group-wise ANOVA-simultaneous component analysis (GASCA) with the aim of obtaining models that are easier to interpret.Methods: GASCA is based on the concept of group-wise sparsity introduced in group-wise principal components analysis where structure to impose sparsity is defined in terms of groups of correlated variables found in the correlation matrices calculated from the effect matrices.Results: The GASCA model, containing only selected subsets of the original variables, is easier to interpret and describes relevant biological processes.Conclusions: GASCA is applicable to any kind of omics data obtained through designed experiments such as, but not limited to, metabolomic, proteomic and gene expression data.

In omics research often high-dimensional data is collected according to an experimental design. Typically, the manipulations involved yield differential effects on subsets of variables. An effective approach to identify those effects is ANOVA-simultaneous component analysis (ASCA), which combines analysis of variance with principal component analysis. So far, pre-treatment in ASCA received hardly any attention, whereas its effects can be huge. In this paper, we describe various strategies for scaling, and identify a rational approach. We present the approaches in matrix algebra terms and illustrate them with an insightful simulated example. We show that scaling directly influences which data aspects are stressed in the analysis, and hence become apparent in the solution. Therefore, the cornerstone for proper scaling is to use a scaling factor that is free from the effect of interest. This implies that proper scaling depends on the effect(s) of interest, and that different types of scaling may be proper for the different effect matrices. We illustrate that different scaling approaches can greatly affect the ASCA interpretation with a real-life example from nutritional research. The principle that scaling factors should be free from the effect of interest generalizes to other statistical methods that involve scaling, as classification methods. Electronic supplementary material The online version of this article (doi:10.1007/s11306-015-0785-8) contains supplementary material, which is available to authorized users.

Background Opisthorchiasis is a parasitic infection caused by the liver flukes of the Opisthorchiidae family. Both experimental and epidemiological data strongly support a role of these parasites in the etiology of the hepatobiliary pathologies and an increased risk of intrahepatic cholangiocarcinoma. Understanding a functional link between the infection and hepatobiliary pathologies requires a detailed description a host-parasite interaction on different levels of biological regulation including the metabolic response on the infection. The last one, however, remains practically undocumented. Here we are describing a host response on Opisthorchiidae infection using a metabolomics approach and present the first exploratory metabolomics study of an experimental model of O. felineus infection. Methodology and Principal findings We conducted a Nuclear Magnetic Resonance (NMR) based longitudinal metabolomics study involving a cohort of 30 animals with two degrees of infection and a control group. An exploratory analysis shows that the most noticeable trend (30% of total variance) in the data was related to the gender differences. Therefore further analysis was done of each gender group separately applying a multivariate extension of the ANOVA—ASCA (ANOVA simultaneous component analysis). We show that in the males the infection specific time trends are present in the main component (43.5% variance), while in the females it is presented only in the second component and covers 24% of the variance. We have selected and annotated 24 metabolites associated with the observed effects and provided a physiological interpretation of the findings. Conclusions The first exploratory metabolomics study an experimental model of O. felineus infection is presented. Our data show that at early stage of infection a response of an organism unfolds in a gender specific manner. Also main physiological mechanisms affected appear rather nonspecific (a status of the metabolic stress) the data provides a set of the hypothesis for a search of the more specific metabolic markers of the Opisthorchiidae infection., Author summary Opisthorchiasis is a parasitic infection caused by the liver flukes of the Opisthorchiidae family (Trematoda; Platyhelminthes). The liver fluke infections trigger development of the hepatobiliary pathologies such as chronic forms of cholecystitis, cholangitis, pancreatitis, and cholelithiasis. However, the most threatening effect of the Opisthorchiidae infection is an increased risk of intrahepatic cholangiocarcinoma. With this work we are getting an insight into a host response on Opisthorchiidae infection using a metabolomics approach. Metabolomics is a post-genomic discipline studying the metabolome. The dynamic character of the metabolome, its ability to change in response to the external stimuli makes it an optimal “readout” for exploratory studies aiming for the description of the systemic responses of an organism. Using this approach we demonstrate that that early response to the O. felineus infection unfolds in a gender-dependent manner. Moreover, with this first exploratory analysis of the metabolic response to O. felineus infection in an animal model we present a subset of the metabolites changing during the early phase of the infection and offer a possible physiological interpretation.

The effect of mango solar drying methods (traditional and tunnel dryers) on the quality of dried mango slices was investigated by visible (VIS) and near-infrared (NIR) spectroscopy combined with the chemometric analysis methods of principal component analysis (PCA) and ANOVA-simultaneous component analysis (ASCA). Five batches of mango were investigated, each subjected to two/three different positions of three different types of dryers: electrical (reference), traditional, and tunnel dryers. The results of the visible and near-infrared spectra showed that the quality of the mango samples obtained from the electrical dryer (reference method) was the most uniform and conserved the highest content of carotenoids and chlorophyll pigments. The samples from the traditional dryer had the highest variation and content of residual water. ASCA analysis of visible and shortwave near-infrared (VIS-NIR) (including color information) showed that the batch effect was most dominant with a significance effect of 47.5%, whereas longwave near-infrared (NIR) spectra (chemistry) showed that the dryer effect was the most dominant with a significance effect of 38.3%. The factor of the fruit positions in the dryers proved not to be significant. The VIS-NIR spectrum is thus well adapted to measure the fruit maturity and the NIR spectrum has great potential to investigate and control the dryer performance. The latter clearly demonstrated that the tunnel dryer provides much more gentle and consistent drying process compared to the traditional dryer. In contrast, the samples from the traditional dryer showed chemical changes/decomposition.

In human metabolic profiling studies, between-subject variability is often the dominant feature and can mask the potential classifications of clinical interest. Conventional models such as principal component analysis (PCA) are usually not effective in such situations and it is therefore highly desirable to find a suitable model which is able to discover the underlying pattern hidden behind the high between-subject variability. In this study we employed two clinical metabolomics data sets as the testing grounds, in which such variability had been observed, and we demonstrate that a proper choice of chemometrics model can help to overcome this issue of high between-subject variability. Two data sets were used to represent two different types of experiment designs. The first data set was obtained from a small-scale study investigating volatile organic compounds (VOCs) collected from chronic wounds using a skin patch device and analysed by thermal desorption-gas chromatography-mass spectrometry. Five patients were recruited and for each patient three sites sampled in triplicate: healthy skin, boundary of the lesion and top of the lesion, the aim was to discriminate these three types of samples based on their VOC profile. The second data set was from a much larger study involving 35 healthy subjects, 47 patients with chronic obstructive pulmonary disease and 33 with asthma. The VOCs in the breath of each subject were collected using a mask device and analysed again by GC–MS with the aim of discriminating the three types of subjects based on breath VOC profiles. Multilevel simultaneous component analysis, multilevel partial least squares for discriminant analysis, ANOVA-PCA, and a novel simplified ANOVA-PCA model—which we have named ANOVA-Mean Centre (ANOVA-MC)—were applied on these two data sets. Significantly improved results were obtained by using these models. We also present a novel validation procedure to verify statistically the results obtained from those models.

Lipidome profile of fluids and tissues is a growing field as the role of lipids as signaling molecules is increasingly understood, relying on an effective and representative extraction of the lipids present. A number of solvent systems suitable for lipid extraction are commonly in use, though no comprehensive investigation of their effectiveness across multiple lipid classes has been carried out. To address this, human LDL from normolipidemic volunteers was used to evaluate five different solvent extraction protocols [Folch, Bligh and Dyer, acidified Bligh and Dyer, methanol (MeOH)-tert-butyl methyl ether (TBME), and hexane-isopropanol] and the extracted lipids were analyzed by LC-MS in a high-resolution instrument equipped with polarity switching. Overall, more than 350 different lipid species from 19 lipid subclasses were identified. Solvent composition had a small effect on the extraction of predominant lipid classes (triacylglycerides, cholesterol esters, and phosphatidylcholines). In contrast, extraction of less abundant lipids (phosphatidylinositols, lyso-lipids, ceramides, and cholesterol sulfates) was greatly influenced by the solvent system used. Overall, the Folch method was most effective for the extraction of a broad range of lipid classes in LDL, although the hexane-isopropanol method was best for apolar lipids and the MeOH-TBME method was suitable for lactosyl ceramides.

The study of nutritional interventions in humans is difficult to assess because the induced metabolic changes are lower than the natural biological variability between subjects. Due to its holistic approach, 1H NMR is one of the preferred technologies for this type of studies, even though it has a very low sensitivity. This work shows how the use of several chemometric algorithms on the measured data compensates for these drawbacks and allows the study of the effects of the nutritional intervention isolating them from the natural variability inherent to human studies. Mild to moderate hypercholesterolemic patients received either placebo or soluble fiber in a low saturated fat diet. Plasma samples were collected at week 0 and week 8. Spectra obtained with NMR equipment were processed with ANOVA simultaneous component analysis (ASCA). The application of clustering techniques revealed different responses based on the patient's basal state, which allowed the identification of responders from non-responders. Results showed a triglyceride level reduction of up to 15% (p = 0.0032), with a higher reduction for those patients with a higher initial lipid profile. Moreover, line-shape fitting techniques applied to the NMR spectra allowed the conclusion that LDL (and VLDL) lipoprotein particles, and more noticeably triglycerides, moved to a profile configuration associated with lower cardiovascular risk. Results shed light on some of the metabolic modifications that husk fiber induces in humans which could not be seen with more conventional data analysis approaches. Our conclusion is that by using the right chemometric techniques it is possible to assess nutritional intervention effects in human NMR human studies despite the low sensitivity and selectivity that the technique offers today.

Metabolomics analysis of oil palm leaves is a promising strategy to prospect new added-value compounds of this underutilized oil industry by-product. Although previous studies had reported some metabolites identified in this matrix, they had been focused on few compounds using conventional analytical techniques. This study aimed to develop a new high throughput method based on metabolomics able to detect a wide range of metabolites classes in Elaeis guineensis leaves. Furthermore, we investigate the effects caused by harvesting/sample preparation steps for the metabolites identification. Metabolites analyses were performed by ultra-high liquid chromatography—mass spectrometry (UHPLC–MS) using both ionization modes, ESI(+)–MS and ESI(−)–MS. ANOVA simultaneous component analysis (ASCA) of the resulting complex multivariate dataset was applied to evaluate metabolic alterations. Identification of major metabolites was performed by high resolution mass spectrometry and MS/MS experiments. A high throughput method based on UHPLC–MS was successfully developed to E. guineensis leaves, detecting from polar to non-polar acid and basic metabolites. According to ASCA, oil palm leaves metabolic fingerprintings have shown influence of transportation/storage and extraction solvent used chosen. In fact, the most significant effect is due to the solvent composition. A total of thirteen metabolites were assigned based on HRMS and MS/MS experiments. However, only seven metabolites identified were previously reported, which represents a potential field to discover new metabolites. Sample preparation steps should be carefully performed in metabolomics studies, because metabolites will be extracted and identified based on transport and solvent of extraction conditions. In this study, we established a reliable analytical protocol, from sample preparation to data analyses, to prospect new metabolites in oil palm leaves. This protocol could be further applied to similar oil-bearing crops.

Saliva is an easy to obtain bodily fluid that is specific to the oral environment. It can be used for metabolomic studies as it is representative of the overall wellbeing of an organism, as well as mouth health and bacterial flora. The metabolomic structure of saliva varies greatly depending on the bacteria present in the mouth as they produce a range of metabolites. In this study we have investigated the metabolomic profiles of human saliva that were obtained using 1H NMR (nuclear magnetic resonance) analysis. 48 samples of saliva were collected from 16 healthy subjects over 3 days. Each sample was split in two and the first half treated with an oral rinse, while the second was left untreated as a control sample. The 96 1H NMR metabolomic profiles obtained in the dataset are affected by three factors, namely 16 subjects, 3 sampling days and 2 treatments. These three factors contribute to the total variation in the dataset. When analysing datasets from saliva using traditional methods such as PCA (principal component analysis), the overall variance is dominated by subjects’ contributions, and we cannot see trends that would highlight the effect of specific factors such as oral rinse. In order to identify these trends, we used methods such as MSCA (multilevel simultaneous component analysis) and ASCA (ANOVA simultaneous component analysis), that provide variance splits according to the experimental factors, so that we could look at the particular effect of treatment on saliva. The analysis of the treatment effect was enhanced, as it was isolated from the overall variance and assessed without confounding factors.

ANOVA-simultaneous component analysis (ASCA) is a recently developed tool to analyze multivariate data. In this paper, we enhance the explorative capability of ASCA by introducing a projection of the observations on the principal component subspace to visualize the variation among the measurements. We compare the significance of experimental effects for ASCA and ANOVA-principal component analysis (PCA), a similar tool to explore multivariate data, by using permutation tests. Furthermore, we quantify the quality of the loadings estimate obtained with ASCA and compare this with the loadings estimate obtained with ANOVA-PCA.

This paper proposes panel concordance analysis (PANCA) as a tool for panel leaders to identify disconsensus between the panelists on the sensory attributes used. PANCA summarizes the sensory data ([products × panelists × replicates] × attributes) by a low-rank approximation which is penalized for disconsensus (disagreement) between the panelists. When all the panelists agree on the sensory attributes used, the disconsensus penalty will have a negligible effect. However, if the assumption of good consensus is not supported by the data, considerable residual errors will arise. Consequently, PANCA can be used to identify difficult sensory attributes or even poor/deviating panelists which requires further training or could call for an alternative data processing strategy. It is also demonstrated that PANCA can be used to apply a multivariate ANOVA decomposition like in ASCA (ANOVA simultaneous component analysis). Theory and applications are explained by means of a real-life example from industrial sensory practice.

Residential wood combustion emissions are one of the major global sources of particulate and gaseous organic pollutants. However, the detailed chemical compositions of these emissions are poorly characterized due to their highly complex molecular compositions, nonideal combustion conditions, and sample preparation steps. In this study, the particulate organic emissions from a masonry heater using three types of wood logs, namely, beech, birch, and spruce, were chemically characterized using thermal desorption in situ derivatization coupled to a GCxGC-ToF/MS system. Untargeted data analyses were performed using the comprehensive measurements. Univariate and multivariate chemometric tools, such as analysis of variance (ANOVA), principal component analysis (PCA), and ANOVA simultaneous component analysis (ASCA), were used to reduce the data to highly significant and wood type-specific features. This study reveals substances not previously considered in the literature as meaningful markers for differentiation among wood types.

Metabolite profiling in combination with multivariate statistics is a sophisticated method for quality assessment of natural products. For the development of a quality control strategy in Traditional Chinese Medicine (TCM), we have measured the metabolite fingerprints of Rehmannia glutinosa by GC-MS. Plants were grown under different climate and soil conditions in a phytotron and were processed by a variable number of repetitive steps to investigate the effects on both growth conditions and processing for material medica of R. glutinosa. The GC-MS data have been analyzed by principal component analysis (PCA) and the new approach of the ANOVA-simultaneous component analysis (ASCA) which can combine the information from a structured data design with multivariate analysis. The results clearly show the effect of the different factors and indicate directions for process improvement. When plants were grown under various temperatures, humidity and light intensities for a short period (3 weeks), no significant changes on studied metabolites were observed. However, significant changes were found between different processing cycles. The present data clearly indicate the importance of strictly controlling processing in R. glutinosa and illustrate the impact of growth conditions. This is the first report on the metabolite profile of R. glutinosa that provides a base for the establishment of a quality control strategy. © Georg Thieme Verlag KG Stuttgart.

Motivation: Datasets resulting from metabolomics or metabolic profiling experiments are becoming increasingly complex. Such datasets may contain underlying factors, such as time (time-resolved or longitudinal measurements), doses or combinations thereof. Currently used biostatistics methods do not take the structure of such complex datasets into account. However, incorporating this structure into the data analysis is important for understanding the biological information in these datasets. Results: We describe ASCA, a new method that can deal with complex multivariate datasets containing an underlying experimental design, such as metabolomics datasets. It is a direct generalization of analysis of variance (ANOVA) for univariate data to the multivariate case. The method allows for easy interpretation of the variation induced by the different factors of the design. The method is illustrated with a dataset from a metabolomics experiment with time and dose factors. Availability: M-files for MATLAB for the algorithm used in this research are available at: http://www-its.chem.uva.nl/research/pac/Software/ or at http://www.bdagroup.nl Contact: asmilde@science.uva.nl

A soft tool for detection of biomarkers in high dimensional data sets has been developed. The tool combines analysis of variance (ANOVA) and principal component analysis (PCA). Covariations are separated using ANOVA into main effects and interaction. The covariances for each effect are combined with the pure error and subjected to PCA. If the main effect is significant compared to the residual error, the first principal component will span this source of variation. This technique avoids rotation of the principal components and when significant the variable loadings are amenable to interpretation. ANOVA–PCA is demonstrated as a tool for optimization of a proteomic assay for biomarkers. Two independent sets of matrix assisted laser desorption/ionization-mass spectra (MALDI-MS) were collected from amniotic fluids. These studies gave consistent biomarkers for premature delivery.

Many advanced metabolomics experiments currently lead to data where a large number of response variables were measured while one or several factors were changed. Often the number of response variables vastly exceeds the sample size and well-established techniques such as multivariate analysis of variance (MANOVA) cannot be used to analyze the data. ANOVA simultaneous component analysis (ASCA) is an alternative to MANOVA for analysis of metabolomics data from an experimental design. In this paper, we show that ASCA assumes that none of the metabolites are correlated and that they all have the same variance. Because of these assumptions, ASCA may relate the wrong variables to a factor. This reduces the power of the method and hampers interpretation. We propose an improved model that is essentially a weighted average of the ASCA and MANOVA models. The optimal weight is determined in a data-driven fashion. Compared to ASCA, this method assumes that variables can correlate, leading to a more realistic view of the data. Compared to MANOVA, the model is also applicable when the number of samples is (much) smaller than the number of variables. These advantages are demonstrated by means of simulated and real data examples. The source code of the method is available from the first author upon request, and at the following github repository: https://github.com/JasperE/regularized-MANOVA.

Data sets resulting from metabolomics, proteomics, or metabolic profiling experiments are usually complex. This type of data contains underlying factors, such as time, doses, or combinations thereof. Classical biostatistics methods do not take into account the structure of such complex data sets. However, incorporating this structure into the data analysis is important for understanding the biological information in these data sets. We describe ANOVA simultaneous component analysis (ASCA), a method capable of dealing with complex multivariate data sets containing an underlying experimental design. It is a generalization of analysis of variance (ANOVA) for univariate data to the multivariate case. The method allows for easy interpretation of the variation induced by the different factors of the design. The method is illustrated with a data set from a metabolomics experiment with time and dose factors.

Metabolite profiling in combination with multivariate statistics is a sophisticated method for quality assessment of natural products. For the development of a quality control strategy in Traditional Chinese Medicine (TCM), we have measured the metabolite fingerprints of Rehmannia glutinosa by GC-MS. Plants were grown under different climate and soil conditions in a phytotron and were processed by a variable number of repetitive steps to investigate the effects on both growth conditions and processing for material medica of R. glutinosa. The GC-MS data have been analyzed by principal component analysis (PCA) and the new approach of the ANOVA-simultaneous component analysis (ASCA) which can combine the information from a structured data design with multivariate analysis. The results clearly show the effect of the different factors and indicate directions for process improvement. When plants were grown under various temperatures, humidity and light intensities for a short period (3 weeks), no significant changes on studied metabolites were observed. However, significant changes were found between different processing cycles. The present data clearly indicate the importance of strictly controlling processing in R. glutinosa and illustrate the impact of growth conditions. This is the first report on the metabolite profile of R. glutinosa that provides a base for the establishment of a quality control strategy. © Georg Thieme Verlag KG Stuttgart.

Metabolite profiling in combination with multivariate statistics is a sophisticated method for quality assessment of natural products. For the development of a quality control strategy in Traditional Chinese Medicine (TCM), we have measured the metabolite fingerprints of Rehmannia glutinosa by GC-MS. Plants were grown under different climate and soil conditions in a phytotron and were processed by a variable number of repetitive steps to investigate the effects on both growth conditions and processing for material medica of R. glutinosa. The GC-MS data have been analyzed by principal component analysis (PCA) and the new approach of the ANOVA-simultaneous component analysis (ASCA) which can combine the information from a structured data design with multivariate analysis. The results clearly show the effect of the different factors and indicate directions for process improvement. When plants were grown under various temperatures, humidity and light intensities for a short period (3 weeks), no significant changes on studied metabolites were observed. However, significant changes were found between different processing cycles. The present data clearly indicate the importance of strictly controlling processing in R. glutinosa and illustrate the impact of growth conditions. This is the first report on the metabolite profile of R. glutinosa that provides a base for the establishment of a quality control strategy. © Georg Thieme Verlag KG Stuttgart.

Recently analysis of variance (ANOVA)-simultaneous component analysis (ASCA) has been introduced as an explorative tool for the analysis of multivariate data with an underlying experimental design [Smilde et al. Bioinformatics 2005; 21: 3043-3048]. This paper focuses on the general methodological framework of ASCA. The drawbacks of other methods for the analysis of this type of data are discussed, as well as the advantages of ASCA above these other methods. Three case studies are used to illustrate the use of ASCA. The relationship between ASCA and several other multivariate data analysis techniques is demonstrated. Finally, possible extensions for ASCA are presented, including multiway analysis and multivariate regression. Copyright (c) 2006 John Wiley & Sons, Ltd.

The analysis of pollen chemical composition is important to many fields, including agriculture, plant physiology, ecology, allergology, and climate studies. Here, the potential of a combination of different spectroscopic and spectrometric methods regarding the characterization of small biochemical differences between pollen samples was evaluated using multivariate statistical approaches. Pollen samples, collected from three populations of the grass Poa alpina, were analyzed using Fourier-transform infrared (FTIR) spectroscopy, Raman spectroscopy, surface enhanced Raman scattering (SERS), and matrix assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS). The variation in the sample set can be described in a hierarchical framework comprising three populations of the same grass species and four different growth conditions of the parent plants for each of the populations. Therefore, the data set can work here as a model system to evaluate the classification and characterization ability of the different spectroscopic and spectrometric methods. ANOVA Simultaneous Component Analysis (ASCA) was applied to achieve a separation of different sources of variance in the complex sample set. Since the chosen methods and sample preparations probe different parts and/or molecular constituents of the pollen grains, complementary information about the chemical composition of the pollen can be obtained. By using consensus principal component analysis (CPCA), data from the different methods are linked together. This enables an investigation of the underlying global information, since complementary chemical data are combined. The molecular information from four spectroscopies was combined with phenotypical information gathered from the parent plants, thereby helping to potentially link pollen chemistry to other biotic and abiotic parameters.

Background Innovative extensions of (M) ANOVA gain common ground for the analysis of designed metabolomics experiments. ASCA is such a multivariate analysis method; it has successfully estimated effects in megavariate metabolomics data from biological experiments. However, rigorous statistical validation of megavariate effects is still problematic because megavariate extensions of the classical F-test do not exist. Methods A permutation approach is used to validate megavariate effects observed with ASCA. By permuting the class labels of the underlying experimental design, a distribution of no-effect is calculated. If the observed effect is clearly different from this distribution the effect is deemed significant Results The permutation approach is studied using simulated data which gave successful results. It was then used on real-life metabolomics data set dealing with bromobenzene-dosed rats. In this metabolomics experiment the dosage and time-interaction effect were validated, both effects are significant. Histological screening of the treated rats' liver agrees with this finding. Conclusion The suggested procedure gives approximate p-values for testing effects underlying metabolomics data sets. Therefore, performing model validation is possible using the proposed procedure.