Metabolite content profiling of bottlenose dolphin exhaled breath

Origin of breath isoprene in humans is revealed via multi-omic investigations

Plants, animals and humans metabolically produce volatile isoprene (C5H8). Humans continuously exhale isoprene and exhaled concentrations differ under various physio-metabolic and pathophysiological conditions. Yet unknown metabolic origin hinders isoprene to reach clinical practice as a biomarker. Screening 2000 individuals from consecutive mass-spectrometric studies, we herein identify five healthy German adults without exhaled isoprene. Whole exome sequencing in these adults reveals only one shared homozygous (European prevalence: <1%) IDI2 stop-gain mutation, which causes losses of enzyme active site and Mg2+-cofactor binding sites. Consequently, the conversion of isopentenyl diphosphate to dimethylallyl diphosphate (DMAPP) as part of the cholesterol metabolism is prevented in these adults. Targeted sequencing depicts that the IDI2 rs1044261 variant (p.Trp144Stop) is heterozygous in isoprene deficient blood-relatives and absent in unrelated isoprene normal adults. Wild-type IDI1 and cholesterol metabolism related serological parameters are normal in all adults. IDI2 determines isoprene production as only DMAPP sources isoprene and unlike plants, humans lack isoprene synthase and its enzyme homologue. Human IDI2 is expressed only in skeletal-myocellular peroxisomes and instant spikes in isoprene exhalation during muscle activity underpins its origin from muscular lipolytic cholesterol metabolism. Our findings translate isoprene as a clinically interpretable breath biomarker towards potential applications in human medicine.

Using Blood Gas Analysis and Capnography to Determine Oxygenation Status in Bottlenose Dolphins (Tursiops truncatus) Following the Deepwater Horizon Oil Spill

Following the Deepwater Horizon (DWH) oil spill in 2010, poor pulmonary health and reproductive failure in bottlenose dolphins (Tursiops truncatus) in the northern Gulf of Mexico were well-documented. One postulated etiology for the increased fetal distress syndrome and pneumonia found in affected perinatal dolphins was maternal hypoxia caused by lung disease. The objective of this study was to evaluate the utility of blood gas analysis and capnography in determining oxygenation status in bottlenose dolphins with and without pulmonary disease. Blood and breath samples were collected from 59 free-ranging dolphins in Barataria Bay, Louisiana (BB), during a capture-release health assessment program, and from 30 managed dolphins from the U.S. Navy Marine Mammal Program in San Diego, CA. The former was the oil-exposed cohort and the latter served as a control cohort with known health histories. Capnography and select blood gas parameters were compared based on the following factors: cohort, sex, age/length class, reproductive status, and severity of pulmonary disease. Animals with moderate-severe lung disease had higher bicarbonate concentrations (p = 0.005), pH (p < 0.001), TCO₂ (p = 0.012), and more positive base excess (p = 0.001) than animals with normal-mild disease. Capnography (ETCO₂) was found to have a weak positive correlation with blood PCO₂ (p = 0.020), with a mean difference of 5.02 mmHg (p < 0.001). Based on these findings, indirect oxygenation measures, including TCO₂, bicarbonate, and pH, show promise in establishing the oxygenation status in dolphins with and without pulmonary disease.

Climate change and cetacean health: impacts and future directions

Climate change directly impacts the foraging opportunities of cetaceans (e.g. lower prey availability), leads to habitat loss, and forces cetaceans to move to other feeding grounds. The rise in ocean temperature, low prey availability and loss of habitat can have severe consequences for cetacean survival, particularly those species that are already threatened or those with a limited habitat range. In addition, it is predicted that the concentration of contaminants in aquatic environments will increase owing to Arctic meltwater and increased rainfall events leading to higher rates of land-based runoff in downstream coastal areas. These persistent and mobile contaminants can bioaccumulate in the ecosystem, and lead to ecotoxicity with potentially severe consequences on the reproductive organs, immune system and metabolism of marine mammals. There is a need to measure and assess the cumulative impact of multiple stressors, given that climate change, habitat alteration, low prey availability and contaminants do not act in isolation. Human-caused perturbations to cetacean foraging abilities are becoming a pervasive and prevalent threat to many cetacean species on top of climate change-associated stressors. We need to move to a greater understanding of how multiple stressors impact the metabolism of cetaceans and ultimately their population trajectory. This article is part of the theme issue 'Nurturing resilient marine ecosystems'.

Untargeted plasma metabolomic analysis of wild bottlenose dolphins (Tursiops truncatus) indicate protein degradation when in poorer health

Cumulative exposure to sub-lethal anthropogenic stressors can affect the health and reproduction of coastal cetaceans and hence their population viability. To date, we do not have a clear understanding of the notion of health for cetaceans in an ecological context; that is, how health status affects the ability of individuals to survive and reproduce. Here, we make use of a unique health-monitoring programme of estuarine bottlenose dolphins in South Carolina and Florida to determine de novo changes in biological pathways, using untargeted plasma metabolomics, depending on the health status of individuals obtained from veterinary screening. We found that individuals that were in a poor health state had lower circulating amino acids pointing towards increased involvement of gluconeogenesis (i.e., new formation of glucose). More mechanistic work is needed to disentangle the interconnection between health and energy metabolism in cetaceans to mediate potential metabolic constraints they may face during periods of stress.

Preservation of vapor samples on adsorbent alumina capillaries and implications for field sampling

Dynamic vapor microextraction (DVME) is a vapor preconcentration method that employs a capillary trap coated with an adsorbent, followed by solvent elution to recover the sample. DVME has been developed for applications in the laboratory, including highly precise vapor pressure measurements, and in the field. When vapor collection is conducted outside the laboratory, samples must almost always undergo some interval of storage representing the time between collection and analysis. This interval may be hours, days, or longer, depending on the situation. Regardless, in all situations there must be confidence that the integrity of the samples is maintained until processing and analysis. In this paper, we present results of two studies that tested the stability of a 50% weathered gasoline headspace sample on alumina PLOT (porous layer open tubular) capillaries stored at room temperature for periods from 24 h up to 20 wk. We used principal component analysis (PCA) to reduce the dimensionality of the chromatographic and mass spectral data and elucidate trends in stability with respect to the complex sample's range of hydrocarbon classes and molecular weights. Both analyses identified changes over storage periods of six weeks or more. The hydrocarbon class analysis, which used selected ion monitoring (SIM) data as input, proved more sensitive to changes over shorter storage periods. Sample integrity was preserved for at least 24 h, but losses, especially of high-volatility compounds, occurred by 168 h (7 d). Near total loss of sample occurred by 20 wk. These findings, which are specific to the sample, adsorbent, and storage conditions, will guide choices in experimental and instrumental design to ensure that data from future field studies is reliable.

Breathomics: Review of Sample Collection and Analysis, Data Modeling and Clinical Applications

Metabolomics research is rapidly gaining momentum in disease diagnosis, on top of other Omics technologies. Breathomics, as a branch of metabolomics is developing in various frontiers, for early and noninvasive monitoring of disease. This review starts with a brief introduction to metabolomics and breathomics. A number of important technical issues in exhaled breath collection and factors affecting the sampling procedures are presented. We review the recent progress in metabolomics approaches and a summary of their applications on the respiratory and non-respiratory diseases investigated by breath analysis. Recent reports on breathomics studies retrieved from Scopus and Pubmed were reviewed in this work. We conclude that analyzing breath metabolites (both volatile and nonvolatile) is valuable in disease diagnoses, and therefore believe that breathomics will turn into a promising noninvasive discipline in biomarker discovery and early disease detection in personalized medicine. The problem of wide variations in the reported metabolite concentrations from breathomics studies should be tackled by developing more accurate analytical methods and sophisticated numerical analytical alogorithms.

Breath Sensors for Health Monitoring

Breath sensors can revolutionize medical diagnostics by on-demand detection and monitoring of health parameters in a noninvasive and personalized fashion. Despite extensive research for more than two decades, however, only a few breath sensors have been translated into clinical practice. Actually, most never even left the scientific laboratories. Here, we describe key challenges that currently impede realization of breath sensors and highlight strategies to overcome them. Specifically, we start with breath marker selection (with emphasis on metabolic and inflammatory markers) and breath sampling. Next, the sensitivity, stability, and selectivity requirements for breath sensors are described. Concepts are elaborated to systematically address these requirements by material design (focusing on chemoresistive metal oxides), orthogonal arrays, and filters. Finally, aspects of portable device integration, user communication, and clinical applicability are discussed.

1H NMR metabolomic analysis of skin and blubber of bottlenose dolphins reveals a functional metabolic dichotomy

The common bottlenose dolphin (Tursiops truncatus) is a carnivorous cetacean that thrives in marine environments, one of the apex predators of the marine food web. They are found in coastal and estuarine ecosystems, which are known to be sensitive to environmental impacts. Dolphins are considered sentinel organisms for monitoring the health of coastal marine ecosystems due to their role as predators that can bioaccumulate contaminants. Although recent studies have focused on capturing the circulating metabolomes of these mammals, and in the context of pollutants and exposures in the marine environment, skin and blubber are important surface and protective tissues that have not been adequately probed for metabolism. Using a proton nuclear magnetic resonance spectroscopy (¹H NMR) based metabolomics approach, we quantified 51 metabolites belonging to 74 different metabolic pathways in the skin and blubber of stranded bottlenose dolphin (n = 4) samples collected at different localities in the Southern Zone coast of Yucatan Peninsula of Mexico. Results indicate that metabolism of skin and blubber are quantitatively very different. These metabolite abundances could help discriminate the tissue-types using supervised partial least square regression discriminant analysis (PLSDA). Further, using hierarchical clustering analysis and random forest analysis of the metabolite abundances, the results pointed to unique metabolites that are important classifiers of the tissue-type. On one hand, the differential metabolic patterns, mainly linking fatty acid metabolism and ketogenic amino acids, seem to constitute a characteristic of blubber, thus pointing to fat synthesis and deposition. On the other hand, the skin showed several metabolites involved in gluconeogenic pathways, pointing towards an active anabolic energy-generating metabolism. The most notable pathways found in both tissues included: urea cycle, nucleotide metabolism, amino acid metabolism, glutathione metabolism among others. Our ¹H NMR metabolomics analysis allowed the quantification of metabolites associated with these two organs, i.e., pyruvic acid, arginine, ornithine, 2-hydroxybutyric acid, 3-hydroxyisobutyric acid, and acetic acid, as discriminatory and classifying metabolites. These results would lead to further understanding of the functional and physiological roles of dolphin skin and blubber metabolism for better efforts in their conservation, as well as useful target biopsy tissues for monitoring of dolphin health conditions in marine pollution and ecotoxicology studies.

Approaches for the isolation and identification of hydrophilic, light-sensitive, volatile and minor natural products

Water-soluble, volatile, minor and photosensitive natural products are yet poorly known, and this review discusses the literature reporting the isolation strategies for some of these metabolites.

Plasma metabolomic analysis in mature female common bottlenose dolphins: profiling the characteristics of metabolites after overnight fasting by comparison with data in beagle dogs

The present study was aimed at determining the characteristics of plasma metabolites in bottlenose dolphins to provide a greater understanding of their metabolism and to obtain information for the health management of cetaceans. Capillary electrophoresis-time-of-flight mass spectrometry (CE-TOFMS) and liquid chromatograph-time-of-flight mass spectrometry (LC-TOFMS) were conducted on plasma samples after overnight fasting from three common bottlenose dolphins as well as three beagle dogs (representative terrestrial carnivores) for comparison. In total, 257 and 227 plasma metabolites were identified in the dolphins and the dogs, respectively. Although a small number of animals were used for each species, the heatmap patterns, a principal component analysis and a cluster analysis confirmed that the composition of metabolites could be segregated from each other. Of 257 compounds detected in dolphin plasma, 24 compounds including branched amino acids, creatinine, urea, and methylhistidine were more abundant than in dogs; 26 compounds including long-chained acyl-carnitines and fatty acids, astaxanthin, and pantothenic acid were detected only in dolphins. In contrast, 25 compounds containing lactic acid and glycerol 3-phosphate were lower in dolphins compared to dogs. These data imply active protein metabolism, differences in usage of lipids, a unique urea cycle, and a low activity of the glycolytic pathway in dolphins.

Quantifying hormones in exhaled breath for physiological assessment of large whales at sea

Exhaled breath analysis is a non-invasive assessment tool that has shown promise in human diagnostics, and could greatly benefit research, management, and conservation of large whales. However, hormone assessment of whale respiratory vapor (blow) has been challenged by variable water content and unknown total volume of collected samples. To advance this technique, we investigated urea (a compound present in narrow range in circulation) as a normalizing factor to correct for blow sample concentration. Normalized progesterone, testosterone, and cortisol concentrations of 100 blow samples from 46 photo-identified North Atlantic right whales (Eubalaena glacialis) were more biologically relevant compared to absolute estimates, varying by sex, age class, or individual. Progesterone was elevated in adult females compared with other cohorts and highest in one independently confirmed pregnant female. For both sexes, testosterone was two-fold higher in reproductively mature whales but studied adult females showed the widest variation. Cortisol was present in relatively low concentrations in blow and demonstrated variation between individual whales, suggesting potential for studies of individual differences in adrenal activity. Incorporation of methodologies that normalize sample concentration are essential for blow hormone analysis of free-swimming whales, and measurement of urea could be used to optimize non-invasive physiological assessment of whales.

Power-efficient self-cleaning hydrophilic condenser surface for portable exhaled breath condensate (EBC) metabolomic sampling

In this work, we present a hydrophilic self-cleaning condenser surface for the collection of biological and environmental aerosol samples. The condenser is installed in a battery-operated hand-held breath sampling device. The device performance is characterized by the collection and analysis of exhaled breath samples from a group of volunteers. The exhaled breath condensate is collected on a subcooled condenser surface, transferred into a storage vial, and its chemical content is analyzed using mass spectrometric methods. The engineered surface supports upon it a continuous condensation cycle, and this allows the collection of liquid samples exceeding the saturation mass/area limit of a plain hydrophilic surface. The condenser surface employs two constituent parameters: a low surface energy barrier to enhance nucleation and condensation efficiency, and a network of surface microstructures to create a self-cleaning mechanism for fluid aggregation into a reservoir. Removal of the liquid condensate from the condenser surface prevents the formation of a thick liquid layer, and thus maintains a continuous condensation cycle with a minimum decrease in heat transfer efficiency as condensation occurs on the surface. The self-cleaning condenser surfaces may have a number of applications in the collection of biological, chemical, or environmental aerosol samples. Sample phase conversion to liquid can facilitate sample manipulation and chemical analysis of matrices with low concentrations. Here, we demonstrate the use of a self-cleaning microcondenser for the collection of exhaled breath condensate with a hand-held portable device. All breath collections with the two devices were performed with the same group of volunteers under UC Davis IRB protocol 63701-3.

New Technologies for Monitoring Marine Mammal Health

Omics technologies have been developed in recent decades and applied to different subjects, although the greatest advancements have been achieved in human biology and disease. Genome sequencing and the exploration of its coding and noncoding regions are rapidly yielding meaningful answers to diverse questions, relating genome information to protein activity to environmental changes. In the past, marine mammal genetic and transcriptional studies have been restricted due to the lack of reference genomes. But the advance of high-throughput sequencing is revolutionizing the life sciences technologies. As long-lived organisms, at the top of the food chain, marine mammals play an important role in marine ecosystems and while their protected status is in favor of conservation of the species, it also complicates the researcher's approach to traditional measurements of health. Omics data generated by high-throughput technologies will represent an important key for improving the scientific basis for understanding both marine mammal and environment health.

Exhaled breath condensate methods adapted from human studies using longitudinal metabolomics for predicting early health alterations in dolphins

Monitoring health conditions is essential to detect early asymptomatic stages of a disease. To achieve this, blood, urine and breath samples are commonly used as a routine clinical diagnostic. These samples offer the opportunity to detect specific metabolites related to diseases and provide a better understanding of their development. Although blood samples are commonly used routinely to monitor health, the implementation of a relatively noninvasive technique, such as exhaled breath condensate (EBC) analysis, may further benefit the well-being of both humans and other animals. EBC analysis can be used to track possible physical or biochemical alterations caused by common diseases of the bottlenose dolphin (Tursiops truncatus), such as infections or inflammatory-mediated processes. We have used an untargeted metabolomic method with liquid chromatography-mass spectrometry analysis of EBC samples to determine biomarkers related to disease development. In this study, five dolphins under human care were followed up for 1 year. We collected paired blood, physical examination information, and EBC samples. We then statistically correlated this information to predict specific health alterations. Three dolphins provided promising case study information about biomarkers related to cutaneous infections, respiratory infections, dental disease, or hormonal changes (pregnancy). The use of complementary liquid chromatography platforms, with hydrophilic interaction chromatography and reverse-phased columns, allowed us to detect a wide spectrum of EBC biomarker compounds that could be related to these health alterations. Moreover, these two analytical techniques not only provided complementary metabolite information but in both cases they also provided promising diagnostic information for these health conditions. Graphical abstract Collection of the exhaled condensed breath from a bottlenose dolphin from U.S. Navy Marine Mammal Program (MMP).

Analytical methodologies for broad metabolite coverage of exhaled breath condensate

Breath analysis has been gaining popularity as a non-invasive technique that is amenable to a broad range of medical uses. One of the persistent problems hampering the wide application of the breath analysis method is measurement variability of metabolite abundances stemming from differences in both sampling and analysis methodologies used in various studies. Mass spectrometry has been a method of choice for comprehensive metabolomic analysis. For the first time in the present study, we juxtapose the most commonly employed mass spectrometry-based analysis methodologies and directly compare the resultant coverages of detected compounds in exhaled breath condensate in order to guide methodology choices for exhaled breath condensate analysis studies. Four methods were explored to broaden the range of measured compounds across both the volatile and non-volatile domain. Liquid phase sampling with polyacrylate Solid-Phase MicroExtraction fiber, liquid phase extraction with a polydimethylsiloxane patch, and headspace sampling using Carboxen/Polydimethylsiloxane Solid-Phase MicroExtraction (SPME) followed by gas chromatography mass spectrometry were tested for the analysis of volatile fraction. Hydrophilic interaction liquid chromatography and reversed-phase chromatography high performance liquid chromatography mass spectrometry were used for analysis of non-volatile fraction. We found that liquid phase breath condensate extraction was notably superior compared to headspace extraction and differences in employed sorbents manifested altered metabolite coverages. The most pronounced effect was substantially enhanced metabolite capture for larger, higher-boiling compounds using polyacrylate SPME liquid phase sampling. The analysis of the non-volatile fraction of breath condensate by hydrophilic and reverse phase high performance liquid chromatography mass spectrometry indicated orthogonal metabolite coverage by these chromatography modes. We found that the metabolite coverage could be enhanced significantly with the use of organic solvent as a device rinse after breath sampling to collect the non-aqueous fraction as opposed to neat breath condensate sample. Here, we show the detected ranges of compounds in each case and provide a practical guide for methodology selection for optimal detection of specific compounds.

Noninvasive Respiratory Metabolite Analysis Associated with Clinical Disease in Cetaceans: A Deepwater Horizon Oil Spill Study

Health assessments of wild cetaceans can be challenging due to the difficulty of gaining access to conventional diagnostic matrices of blood, serum and others. While the noninvasive detection of metabolites in exhaled breath could potentially help to address this problem, there exists a knowledge gap regarding associations between known disease states and breath metabolite profiles in cetaceans. This technology was applied to the largest marine oil spill in U.S. history (The 2010 Deepwater Horizon oil spill in the Gulf of Mexico). An accurate analysis was performed to test for associations between the exhaled breath metabolome and sonographic lung abnormalities as well as hematological, serum biochemical, and endocrine hormone parameters. Importantly, metabolites consistent with chronic inflammation, such as products of lung epithelial cellular breakdown and arachidonic acid cascade metabolites were associated with sonographic evidence of lung consolidation. Exhaled breath condensate (EBC) metabolite profiles also correlated with serum hormone concentrations (cortisol and aldosterone), hepatobiliary enzyme levels, white blood cell counts, and iron homeostasis. The correlations among breath metabolites and conventional health measures suggest potential application of breath sampling for remotely assessing health of wild cetaceans. This methodology may hold promise for large cetaceans in the wild for which routine collection of blood and respiratory anomalies are not currently feasible.

Human breath metabolomics using an optimized non-invasive exhaled breath condensate sampler

Exhaled breath condensate (EBC) analysis is a developing field with tremendous promise to advance personalized, non-invasive health diagnostics as new analytical instrumentation platforms and detection methods are developed. Multiple commercially-available and researcher-built experimental samplers are reported in the literature. However, there is very limited information available to determine an effective breath sampling approach, especially regarding the dependence of breath sample metabolomic content on the collection device design and sampling methodology. This lack of an optimal standard procedure results in a range of reported results that are sometimes contradictory. Here, we present a design of a portable human EBC sampler optimized for collection and preservation of the rich metabolomic content of breath. The performance of the engineered device is compared to two commercially available breath collection devices: the RTube^™ and TurboDECCS. A number of design and performance parameters are considered, including: condenser temperature stability during sampling, collection efficiency, condenser material choice, and saliva contamination in the collected breath samples. The significance of the biological content of breath samples, collected with each device, is evaluated with a set of mass spectrometry methods and was the primary factor for evaluating device performance. The design includes an adjustable mass-size threshold for aerodynamic filtering of saliva droplets from the breath flow. Engineering an inexpensive device that allows efficient collection of metalomic-rich breath samples is intended to aid further advancement in the field of breath analysis for non-invasive health diagnostic. EBC sampling from human volunteers was performed under UC Davis IRB protocol 63701-3 (09/30/2014-07/07/2017).

Enhanced non-invasive respiratory sampling from bottlenose dolphins for breath metabolomics measurements

Chemical analysis of exhaled breath metabolites is an emerging alternative to traditional clinical testing for many physiological conditions. The main advantage of breath analysis is its inherent non-invasive nature and ease of sample collection. Therefore, there exists a great interest in further development of this method for both humans and animals. The physiology of cetaceans is exceptionally well suited for breath analysis due to their explosive breathing behavior and respiratory tract morphology. At the present time, breath analysis in cetaceans has very limited practical applications, in large part due to lack of widely adopted sampling device(s) and methodologies that are well-standardized. Here, we present an optimized design and the operating principles of a portable apparatus for reproducible collection of exhaled breath condensate from small cetaceans, such as bottlenose dolphins (Tursiops truncatus). The device design is optimized to meet two criteria: standardized collection and preservation of information-rich metabolomic content of the biological sample, and animal comfort and ease of breath sample collection. The intent is to furnish a fully-benchmarked technology that can be widely adopted by researchers and conservationists to spur further developments of breath analysis applications for marine mammal health assessments.

Get the most out of blow hormones: validation of sampling materials, field storage and extraction techniques for whale respiratory vapour samples

Studies are progressively showing that vital physiological data may be contained in the respiratory vapour (blow) of cetaceans. Nonetheless, fundamental methodological issues need to be addressed before hormone analysis of blow can become a reliable technique. In this study, we performed controlled experiments in a laboratory setting, using known doses of pure parent hormones, to validate several technical factors that may play a crucial role in hormone analyses. We evaluated the following factors: (i) practical field storage of samples on small boats during daylong trips; (ii) efficiency of hormone extraction methods; and (iii) assay interference of different sampler types (i.e. veil nylon, nitex nylon mesh and polystyrene dish). Sampling materials were dosed with mock blow samples of known mixed hormone concentrations (progesterone, 17β-estradiol, testosterone, cortisol, aldosterone and triiodothyronine), designed to mimic endocrine profiles characteristic of pregnant females, adult males, an adrenal glucocorticoid response or a zero-hormone control (distilled H2O). Results showed that storage of samples in a cooler on ice preserved hormone integrity for at least 6 h (P = 0.18). All sampling materials and extraction methods yielded the correct relative patterns for all six hormones. However, veil and nitex mesh produced detectable assay interference (mean 0.22 ± 0.04 and 0.18 ± 0.03 ng/ml, respectively), possibly caused by some nylon-based component affecting antibody binding. Polystyrene dishes were the most efficacious sampler for accuracy and precision (P < 0.001), but required an ethanol rinse for improved progesterone recovery (increased 81%; P < 0.001). Awareness of assay interference from exogenous materials is crucial to future studies. This study establishes critical groundwork to help ensure that hormones can be measured accurately in samples obtained from field collections of whale blow.

PCA as a practical indicator of OPLS-DA model reliability

BACKGROUND

Principal Component Analysis (PCA) and Orthogonal Projections to Latent Structures Discriminant Analysis (OPLS-DA) are powerful statistical modeling tools that provide insights into separations between experimental groups based on high-dimensional spectral measurements from NMR, MS or other analytical instrumentation. However, when used without validation, these tools may lead investigators to statistically unreliable conclusions. This danger is especially real for Partial Least Squares (PLS) and OPLS, which aggressively force separations between experimental groups. As a result, OPLS-DA is often used as an alternative method when PCA fails to expose group separation, but this practice is highly dangerous. Without rigorous validation, OPLS-DA can easily yield statistically unreliable group separation.

METHODS

A Monte Carlo analysis of PCA group separations and OPLS-DA cross-validation metrics was performed on NMR datasets with statistically significant separations in scores-space. A linearly increasing amount of Gaussian noise was added to each data matrix followed by the construction and validation of PCA and OPLS-DA models.

RESULTS

With increasing added noise, the PCA scores-space distance between groups rapidly decreased and the OPLS-DA cross-validation statistics simultaneously deteriorated. A decrease in correlation between the estimated loadings (added noise) and the true (original) loadings was also observed. While the validity of the OPLS-DA model diminished with increasing added noise, the group separation in scores-space remained basically unaffected.

CONCLUSION

Supported by the results of Monte Carlo analyses of PCA group separations and OPLS-DA cross-validation metrics, we provide practical guidelines and cross-validatory recommendations for reliable inference from PCA and OPLS-DA models.

Study of exhaled breath condensate sample preparation for metabolomics analysis by LC-MS/MS in high resolution mode

Metabolomic analysis of exhaled breath condensate (EBC) requires an unavoidable sample preparation step because of the low concentration of its components, and potential cleanup for possible interferents. Sample preparation based on protein precipitation (PP), solid-phase extraction (SPE) by hydrophilic and lipophilic sorbents or lyophilization has demonstrated that the analytical sample from the last is largely the best because lyophilization allows reconstitution in a volume as small as required (preconcentration factors up to 80-times with respect to the original sample), thus doubling the number of detected compounds as compared with the other alternatives (47 versus 25). In addition, PP and/or SPE cleanup are unnecessary as no effect from the EBC components removed by these steps appears in the chromatograms. The total 49 EBC compounds tentatively identified and confirmed by MS/MS in this research include amino acids, fatty acids, fatty amides, fatty aldehydes, sphingoid bases, oxoanionic compounds, imidazoles, hydroxy acids and aliphatic acyclic acids.