Agilent Solutions For Metabolomics EMERGING INSIGHTS

Agilent Solutions for MetabolomicsEMERGING INSIGHTS

Understanding Metabolic FingerprintsA Powerful Way to Investigate BiologyWhat is Metabolomics?Metabolomics is the study of the metabolite content of a cell orwhole organism. Metabolomics studies allow researchers to viewbiological systems in a way that is different from but complementaryto genomics, transcriptomics, and proteomics studies. It is a powerful,emerging discipline with a broad range of applications, includingbasic research, clinical research, drug development, environmentaltoxicology, crop optimization, and food science.What are Metabolites?Metabolites―small organic molecules―are important modulators,substrates, byproducts, and building blocks of many differentbiological processes. Because of this, the presence or absenceof specific metabolites in a cell or sample provides importantinformation about the physiological and functional status of thebiological system or test sample. The accumulation of a specificmetabolite could signal a defect in a pathway, activation of asignal response pathway, or optimization of a biosynthetic pathway.2At Agilent, we are collaborating with leadingmetabolomics researchers—the scientistswho are developing the next generationof metabolomics research techniques andtools—and incorporating their developmentsinto robust solutions that simplify yourmetabolomics research. We offer acomprehensive line of high-performanceGC/MS and LC/MS instruments, providingthe renowned Agilent performance andreliability that is required for making rapid,high-quality metabolomics measurements.Each instrument uses the same data analysissoftware, creating a common user experiencefor experiments that require multiple massspectrometry configurations. Furthermore,the processed data can be analyzed usingAgilent Mass Profiler Professional (MPP)software, a powerful statistical analysis anddata visualization tool that quickly allows youto find and extract meaningful results fromyour data. You can then project your dataonto curated pathways using the powerfulPathway Architect software (an optionalmodule for MPP).

Agilent Enables Metabolomics Research for aVariety of ApplicationsAgilent offers researchers a comprehensive portfolio of metabolomics reagents, columns,instruments, and software to support metabolomics experiments with a number ofapplications including:Basic and Clinical Research Identify and validate metabolite biomarkersthat correlate with disease states as wellas provide fundamental insights into biologyAgricultureIdentify and understand metabolicpathways to optimize crop development,yield improvement, and pesticide/herbicide resistanceFood/NutritionIdentify the presence or absence ofmetabolites that correlate with major traitssuch as food quality, authenticity, taste, andnutritional value, and aid in the developmentof nutraceuticalsPharmaceuticalIdentify metabolites and markers of toxicityfor drug discovery and developmentEnvironmentalIdentify metabolites that relate to theeffects of chemicals and other stressorsin the environment on a biological systemBiofuelsIdentify metabolite profiles to optimizefermentation processes and biofuel production“.we can measure, inmetabolomics, the entire smallmolecule component of abiological sample. And whatthis does is it gives us a pictureat the biochemical level of whatthe physiological status of theorganism or sample was at thetime that it was collected. Andthis gives us a window intothe actual functional state ofthe cell in some ways that isvery different from either theproteomic, or the transcriptomic,or the genomic points of view.”- Chris Beecher, Ph.D.,Chief Scientific OfficerNextGen Metabolomics3

USING THE POWER OF METABOLOMICSWhether you are conducting discovery metabolomics studies or targetedmetabolomics studies, Agilent’s metabolomics portfolio and knowledgeablescientists can help you quickly and reliably obtain and analyze the data you need.Discovery MetabolomicsDiscovery metabolomics experiments involve examining an untargeted suite of metabolites, finding the ones with statistically significantvariations in abundance within a set of experimental versus control samples, and determining their chemical structure. Pathway analysis allowsthe researcher to connect the metabolite with the biological process or condition.Separationand detectionFeature findingand quantitationAlignment andstatistical analysisMassHunter softwareIdentificationPathway analysisLC/MSGC/MSMPP softwareAgilent solutions for discovery metabolomics4Analysis and visualizationCompound identificationPathway Architect

GC/MSOVERLAPLC/MSAlkylsilyl derivativesEicosanoidsEssential sFlavanoidsLipidsAlcoholsAlkaloidsAmino acidsCatecholaminesFatty acidsPhenolicsPolar organicsProstaglandinsSteroidsOrganic acidsOrganic aminesNucleosidesIonic speciesNucleotidesPolyaminesLess polarMore polarChemical classes suitable for GC/MS versus LC/MSAgilent helps you overcome challenges inperforming discovery metabolomics research: Reproducibly track unknowns from sampleto sample with MS systems that providehighly reproducible measurement of massand retention time. Accurately measure abundances in eachsample to enable reliable comparisonof metabolite amounts when standardscannot be used. Find features of interest with tools thatenable you to review and edit yourresults: AMDIS (GC/MS) or MassHunterMolecular Feature Extractor (LC/MS). Identify unknown compounds usingchemical databases integrated withAgilent MassHunter: Agilent FiehnGC/MS RTL Metabolomics Library andMETLIN Personal compound databaseand MS/MS spectral library. Effectively analyze and compare multiplesamples with simple or advanced statisticalanalysis and visualization tools availablein MPP. MPP analyzes both GC/MS andLC/MS data. Evaluate MS data in a biologicalcontext using the optional MPP PathwayArchitect module.For discovery metabolomics, Agilent GC/MS(single quadrupole and Q-TOF) and LC/MS(TOF and Q-TOF) systems are designed todeliver high-performance data with thereproducibility you need for large sample sets.5

Targeted MetabolomicsTargeted metabolomics experiments focus on validation, and use a large number of samples to accurately measure the abundance of previouslyidentified metabolites. It is highly quantitative and usually requires the use of analytical standards.Separation and detectionMRM quantitationPathway analysisMPP softwareLC/MSGC/MSMassHunter softwareStatistical analysisAgilent solutions for targeted metabolomics research6Compound identificationAnalysis and visualizationPathway Architect

Agilent helps you overcome challenges inperforming targeted metabolomics research: Detect low-abundance targets in thepresence of high-abundance metaboliteswith Agilent’s MS systems that offer highsensitivity over a wide dynamic range. Maintain low coefficients of variation(CV), enabling reliable quantitation oflarge sample sets. Rapidly and efficiently analyze largesample sets with MS systems thatprovide robust performance and fastdata acquisition speeds to keep up withfast chromatography. Easily review methods and data to enablebatch processing of large sample sets. Effectively analyze and compare multiplesamples with simple or advancedstatistical analysis and visualization toolsavailable in MPP software, and revalidatepathways proposed by discoverymetabolomics studies.For targeted metabolomics, Agilent’s triplequadrupole LC/MS and GC/MS systemsprovide sensitive detection over a largedynamic range, and offer the reproducibilityand robustness needed to handle largesample sets. Together with MassHunterQuantitative Analysis reporting and MPPanalysis and visualization tools, Agilent’stargeted metabolomics solutions offerunprecedented productivity for large,multi-compound batches.MPP software allows you to identify correlations in your data through a number of clustering methods including hierarchical clustering (shown here). Hierarchical clusteringconnects similar abundance profiles together in a group within a tree structure. The dendrogram view reveals the relationships between mass entities in one dimension andbetween samples in the other dimension. In this example, rat chow diets with differing bean supplements show similarities in abundance profiles for the replicate samples.7

Software Tailored for YourMetabolomics Research NeedsWhether you are conducting discoveryor targeted metabolomics research, youcan analyze your data using the same,powerful software package, Mass ProfilerProfessional (MPP).With MPP, you can compare and visualizedata from large sample sets. Meta datacan be added to the analysis to help youfind relationships in complex experimentaldesigns. You can also normalize, align,and compare data taken from multipleinstruments, a critical feature for laboratoriesrunning multiple metabolomics experiments.MPP makes it easy to identify importantdifferences in the type and relative amountof metabolites present in different samples,facilitating your ability to place the data into abiological context. You can identify statisticallysignificant differences using ANOVA, PCA,clustering, volcano plot, hierarchical clustering,class predictions, or customize analysis bywriting your own R scripts.Powerful, easy-to-use workflow-guided MPP software allows you to combine multiple experiment types using asingle software platform.Within the MPP environment, you canalso determine the chemical identity ofmetabolites by searching their retentiontime and spectra against the METLINPersonal compound database and library orthe Agilent Fiehn GC/MS RTL MetabolomicsLibrary. In addition, for accurate-mass data,the ID Browser can calculate empiricalformulas using spectral data. Empiricalformulas can be combined with accuratemass databases to increase confidencein compound identification.MPP software helps you elucidate differences in your GC/MS and LC/MS experiments. Agilent’s Mass ProfilerProfessional software includes multivariate analytical tools, such as principal component analysis, ANOVA,clustering algorithms, and class prediction, to efficiently turn large sample sets into meaningful information.8