partial least-squares-discriminant analysis
Dotaz
Zobrazit nápovědu
Automated head-space solid-phase microextraction (HS-SPME)-based sampling procedure, coupled to gas chromatography-time-of-flight mass spectrometry (GC-TOFMS), was developed and employed for obtaining of fingerprints (GC profiles) of beer volatiles. In total, 265 speciality beer samples were collected over a 1-year period with the aim to distinguish, based on analytical (profiling) data, (i) the beers labelled as Rochefort 8; (ii) a group consisting of Rochefort 6, 8, 10 beers; and (iii) Trappist beers. For the chemometric evaluation of the data, partial least squares discriminant analysis (PLS-DA), linear discriminant analysis (LDA), and artificial neural networks with multilayer perceptrons (ANN-MLP) were tested. The best prediction ability was obtained for the model that distinguished a group of Rochefort 6, 8, 10 beers from the rest of beers. In this case, all chemometric tools employed provided 100% correct classification. Slightly worse prediction abilities were achieved for the models "Trappist vs. non-Trappist beers" with the values of 93.9% (PLS-DA), 91.9% (LDA) and 97.0% (ANN-MLP) and "Rochefort 8 vs. the rest" with the values of 87.9% (PLS-DA) and 84.8% (LDA) and 93.9% (ANN-MLP). In addition to chromatographic profiling, also the potential of direct coupling of SPME (extraction/pre-concentration device) with high-resolution TOFMS employing a direct analysis in real time (DART) ion source has been demonstrated as a challenging profiling approach.
BACKGROUND: Metabolomics is becoming an important tool in clinical research and the diagnosis of human diseases. It has been used in the diagnosis of inherited metabolic disorders with pronounced biochemical abnormalities. The aim of this study was to determine if it could be applied in the diagnosis of inherited metabolic disorders (IMDs) with less clear biochemical profiles from urine samples using an untargeted metabolomic approach. METHODS: A total of 14 control urine samples and 21 samples from infants with cystinuria, maple syrup urine disease, adenylosuccinate lyase deficiency and galactosemia were tested. Samples were analyzed by liquid chromatography on aminopropyl column in aqueous normal phase separation system using gradient elution of acetonitrile/ammonium acetate. Detection was performed by time-of-flight mass spectrometer fitted with electrospray ionisation in positive mode. The data were statistically processed using principal component analysis (PCA), principal component discriminant function analysis (PCA-DFA) and partial least squares (PLS) regression. RESULTS: All patient samples were first distinguished from controls using unsupervised PCA. Discrimination of the patient samples was then unambiguously verified using supervised PCA-DFA. Known markers of the diseases in question were successfully confirmed and a potential new marker emerged from the PLS regression. CONCLUSION: This study showed that untargeted metabolomics can be applied in the diagnosis of mild IMDs with less clear biochemical profiles.
- MeSH
- adenylsukcinátlyasa nedostatek MeSH
- analýza hlavních komponent MeSH
- autistická porucha diagnóza MeSH
- biologické markery moč MeSH
- cystinurie diagnóza MeSH
- dítě MeSH
- dospělí MeSH
- galaktosemie diagnóza MeSH
- hmotnostní spektrometrie metody MeSH
- kojenec MeSH
- lidé MeSH
- metabolické nemoci diagnóza MeSH
- metabolomika metody MeSH
- mladiství MeSH
- mladý dospělý MeSH
- nemoc s močí javorového sirupu diagnóza MeSH
- poruchy metabolismu purinů a pyrimidinů diagnóza MeSH
- studie případů a kontrol MeSH
- vysokoúčinná kapalinová chromatografie metody MeSH
- Check Tag
- dítě MeSH
- dospělí MeSH
- kojenec MeSH
- lidé MeSH
- mladiství MeSH
- mladý dospělý MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Ambient mass spectrometry employing a direct analysis in real time (DART) ion source coupled to a medium high-resolution/accurate mass time-of-flight mass spectrometer (TOFMS) was used as a rapid tool for metabolomic fingerprinting to study the effects of supplemental feeding with cereals (triticale) on the composition of muscle metabolites of common carp (Cyprinus carpio L.). First, the sample extraction and DART-TOFMS instrumental conditions were optimized to obtain the broadest possible representation of ionizable compounds occurring in the extracts obtained from common carp muscle. To this end, a simultaneous (all-in-one) extraction procedure was developed employing water and cyclohexane mixture as the extraction solvents. Under these conditions both polar as well as non-polar metabolites were isolated within a single extraction step. Next, the metabolomic fingerprints (mass spectra) of a large set of common carp muscle extracts were acquired. Finally, the experimental data were statistically evaluated using principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA). Using this approach, differentiation of common carp muscle in response to dietary supplementation (feeding with and without cereals) was feasible. Correct classification was obtained based on the assessment of polar and as well as non-polar extracts fingerprints. The current study showed that DART-TOFMS metabolomic fingerprinting represents a rapid and powerful analytical strategy enabling differentiation of common carp muscles according to feeding history by recording metabolomic fingerprints of ionizable components under the conditions of ambient MS.
- MeSH
- analýza hlavních komponent MeSH
- cyklohexany MeSH
- dieta MeSH
- extrakce kapalina-kapalina MeSH
- jedlá semena * MeSH
- kapři růst a vývoj metabolismus MeSH
- kosterní svaly chemie metabolismus MeSH
- metabolom * MeSH
- metoda nejmenších čtverců MeSH
- potravní doplňky * MeSH
- rozpouštědla MeSH
- spektrometrie hmotnostní - ionizace laserem za účasti matrice metody MeSH
- voda MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Corylus avellana L. (Betulaceae) leaves, consumed as infusion, are used in traditional medicine, for the treatment of hemorrhoids, varicose veins, phlebitis, and edema due to their astringent, vasoprotective, and antiedema properties. In previous works we reported from the leaves of Corylus avellana cv. "Tonda di Giffoni" diarylheptanoid derivatives, a class of plant secondary metabolites with a wide variety of bioactivities. With the aim to give an interesting and economically feasible opportunity to C. avellana leaves as source of functional ingredients for pharmaceutical and cosmetic formulations, "green" extracts were prepared by employing "eco-friendly" extraction protocols as maceration, infusion and SLDE-Naviglio extraction. Metabolite profiles of the extracts were obtained by 1H NMR experiments and data were processed by multivariate statistical analysis to highlight differences in the extracts and to evidence the extracts with the highest concentrations of bioactive metabolites. Based on the NMR data, a total of 31 compounds were identified. The metabolite variation among the extracts was evaluated using Principle Component Analysis (PCA) and Partial Least Squares-Discriminant Analysis (PLS-DA). Furthermore, the total phenolic content of the extracts was measured by Folin-Ciocalteu colorimetric assay and the antioxidant activity of extracts was assayed by the spectrophotometric tests DPPH• and ABTS and by an in vitro test based on the evaluation of cellular reactive oxygen species production stimulated by pyocyanin.
- MeSH
- fenoly analýza farmakologie MeSH
- lidé MeSH
- líska chemie metabolismus MeSH
- listy rostlin chemie MeSH
- metabolomika metody MeSH
- nukleární magnetická rezonance biomolekulární metody MeSH
- protonová magnetická rezonanční spektroskopie metody MeSH
- pyokyanin farmakologie MeSH
- reaktivní formy kyslíku metabolismus MeSH
- rostlinné extrakty analýza chemie farmakologie MeSH
- scavengery volných radikálů analýza farmakologie MeSH
- technologie zelené chemie metody MeSH
- THP-1 buňky MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
RATIONALE: The goal of this work is the comparison of differences in the lipidomic compositions of human cell lines derived from normal and cancerous breast tissues, and tumor vs. normal tissues obtained after the surgery of breast cancer patients. METHODS: Hydrophilic interaction liquid chromatography/electrospray ionization mass spectrometry (HILIC/ESI-MS) using the single internal standard approach and response factors is used for the determination of relative abundances of individual lipid species from five lipid classes in total lipid extracts of cell lines and tissues. The supplementary information on the fatty acyl composition is obtained by gas chromatography/mass spectrometry (GC/MS) of fatty acid methyl esters. Multivariate data analysis (MDA) methods, such as nonsupervised principal component analysis (PCA), hierarchical clustering analysis (HCA) and supervised orthogonal partial least-squares discriminant analysis (OPLS-DA), are used for the visualization of differences between normal and tumor samples and the correlation of similarity between cell lines and tissues either for tumor or normal samples. RESULTS: MDA methods are used for differentiation of sample groups and also for identification of the most up- and downregulated lipids in tumor samples in comparison to normal samples. Observed changes are subsequently generalized and correlated with data from tumor and normal tissues of breast cancer patients. In total, 123 lipid species are identified based on their retention behavior in HILIC and observed ions in ESI mass spectra, and relative abundances are determined. CONCLUSIONS: MDA methods are applied for a clear differentiation between tumor and normal samples both for cell lines and tissues. The most upregulated lipids are phospholipids (PL) with a low degree of unsaturation (e.g., 32:1 and 34:1) and also some highly polyunsaturated PL (e.g., 40:6), while the most downregulated lipids are PL containing polyunsaturated fatty acyls (e.g., 20:4), plasmalogens and ether lipids. Copyright © 2016 John Wiley & Sons, Ltd.
- MeSH
- analýza hlavních komponent MeSH
- chromatografie kapalinová metody MeSH
- hmotnostní spektrometrie s elektrosprejovou ionizací metody MeSH
- hydrofobní a hydrofilní interakce MeSH
- lidé MeSH
- lipidy analýza MeSH
- multivariační analýza MeSH
- nádorové buněčné linie MeSH
- nádory prsu chemie metabolismus MeSH
- prsy chemie metabolismus MeSH
- Check Tag
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
Although the identification of animal species and muscles have been reported previously, no studies have been found on the use of NIR spectroscopy to identify individual animals from the analysis of commercial meat cuts. The aim of this study was to evaluate the use of a portable near infrared (NIR) instrument combined with classical chemometrics methods [principal component analysis (PCA) and partial least squares discriminant analysis PLS-DA)] to identify the origin of individual goat animals using the spectral signature of their commercial cut. Samples were collected from several carcasses (6 commercial cuts x 24 animals) sourced from a commercial abattoir in Queensland (Australia). The NIR spectra of the samples were collected using a portable NIR instrument in the wavelength range between 950 and 1600 nm. Overall, the PLS-DA models correctly classify 82% and 79% of the individual goat samples using either the goat rack or loin cut samples, respectively. The study demonstrated that NIR spectroscopy was able to identify individual goat animals based on the spectra properties of some of the commercial cut samples analysed (e.g. loin and rack). These results showed the potential of this technique to identify individual animals as an alternative to other laboratory methods and techniques commonly used in meat traceability.
- Publikační typ
- časopisecké články MeSH
Ultra high performance liquid chromatography with quadrupole/time-of-flight mass spectrometry was applied to evaluate the potential of nontarget metabolomic fingerprinting in order to distinguish Fusarium-infected and control barley samples. First, the sample extraction and instrumental conditions were optimized to obtain the broadest possible representation of polar/medium-polar compounds occurring in extracts obtained from barley grain samples. Next, metabolomic fingerprints of extracts obtained from nine barley varieties were acquired under ESI conditions in both positive and negative mode. Each variety of barley was tested in two variants: artificially infected by Fusarium culmorum at the beginning of heading and a control group (no infection). In addition, the dynamics of barley infection development was monitored using this approach. The experimental data were statistically evaluated by principal component analysis, hierarchical clustering analysis, and orthogonal partial least-squares discriminant analysis. The differentiation of barley in response to F. culmorum infection was feasible using this metabolomics-based method. Analysis in positive mode provided a higher number of molecular features as compared to that performed under negative mode setting. However, the analysis in negative mode permitted the detection of deoxynivalenol and deoxynivalenol-3-glucoside considered as resistance-indicator metabolites in barley.
- MeSH
- analýza hlavních komponent MeSH
- Fusarium fyziologie MeSH
- hmotnostní spektrometrie MeSH
- ječmen (rod) metabolismus mikrobiologie MeSH
- metabolomika * MeSH
- metoda nejmenších čtverců MeSH
- nemoci rostlin mikrobiologie MeSH
- shluková analýza MeSH
- vysokoúčinná kapalinová chromatografie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Cannabis sativa L. plants produce a diverse array of secondary metabolites. Cannabis cell cultures were treated with jasmonic acid (JA) and pectin as elicitors to evaluate their effect on metabolism from two cell lines using NMR spectroscopy and multivariate data analysis. According to principal component analysis (PCA) and partial least square-discriminant analysis (PLS-DA), the chloroform extract of the pectin-treated cultures were more different than control and JA-treated cultures; but in the methanol/water extract the metabolome of the JA-treated cells showed clear differences with control and pectin-treated cultures. Tyrosol, an antioxidant metabolite, was detected in cannabis cell cultures. The tyrosol content increased after eliciting with JA.
- MeSH
- buněčné extrakty chemie izolace a purifikace MeSH
- Cannabis chemie metabolismus MeSH
- cyklopentany metabolismus MeSH
- fenethylalkohol analogy a deriváty analýza MeSH
- kultivované buňky MeSH
- magnetická rezonanční spektroskopie MeSH
- metabolom MeSH
- oxylipiny metabolismus MeSH
- pektiny metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
In recent years, several efforts have been made to develop quick and low cost bacterial identification methods. Genotypic methods, despite their accuracy, are laborious and time consuming, leaving spectroscopic methods as a potential alternative. Mass and infrared spectroscopy are among the most reconnoitered techniques for this purpose, with Raman having been practically unexplored. Some species of the bacterial genus Acinetobacter are recognized as etiological agents of nosocomial infections associated with high rates of mortality and morbidity, which makes their accurate identification important. The goal of this study was to assess the ability of Raman spectroscopy to discriminate between 16 Acinetobacter species belonging to two phylogroups containing taxonomically closely related species, that is, the Acinetobacter baumannii-Acinetobacter calcoaceticus complex (six species) and haemolytic clade (10 species). Bacterial spectra were acquired without the need for any sample pre-treatment and were further analyzed with multivariate data analysis, namely partial least squares discriminant analysis (PLSDA). Species discrimination was achieved through a series of sequential PLSDA models, with the percentage of correct species assignments ranging from 72.1% to 98.7%. The obtained results suggest that Raman spectroscopy is a promising alternative for identification of Acinetobacter species.
- MeSH
- Acinetobacter baumannii chemie klasifikace izolace a purifikace MeSH
- Acinetobacter calcoaceticus chemie klasifikace izolace a purifikace MeSH
- bakteriologické techniky MeSH
- infekce spojené se zdravotní péčí diagnóza mikrobiologie MeSH
- klasifikace MeSH
- lidé MeSH
- Ramanova spektroskopie * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Nuclear magnetic resonance (NMR) metabolomics was used for identification of metabolic changes in pancreatic cancer (PC) blood plasma samples when compared to healthy controls or diabetes mellitus patients. An increased number of PC samples enabled a subdivision of the group according to individual PC stages and the construction of predictive models for finer classification of at-risk individuals recruited from patients with recently diagnosed diabetes mellitus. High-performance values of orthogonal partial least squares (OPLS) discriminant analysis were found for discrimination between individual PC stages and both control groups. The discrimination between early and metastatic stages was achieved with only 71.5% accuracy. A predictive model based on discriminant analyses between individual PC stages and the diabetes mellitus group identified 12 individuals out of 59 as at-risk of development of pathological changes in the pancreas, and four of them were classified as at moderate risk.
- MeSH
- diabetes mellitus * MeSH
- diskriminační analýza MeSH
- lidé MeSH
- magnetická rezonanční spektroskopie MeSH
- metabolomika * MeSH
- pankreas MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
