Metabolism has an essential role in biological systems. Identification and quantitation of the compounds in the metabolome is defined as metabolic profiling, and it is applied to define metabolic changes related to genetic differences, environmental influences and disease or drug perturbations. Chromatography-mass spectrometry (MS) platforms are frequently used to provide the sensitive and reproducible detection of hundreds to thousands of metabolites in a single biofluid or tissue sample. Here we describe the experimental workflow for long-term and large-scale metabolomic studies involving thousands of human samples with data acquired for multiple analytical batches over many months and years. Protocols for serum- and plasma-based metabolic profiling applying gas chromatography-MS (GC-MS) and ultraperformance liquid chromatography-MS (UPLC-MS) are described. These include biofluid collection, sample preparation, data acquisition, data pre-processing and quality assurance. Methods for quality control-based robust LOESS signal correction to provide signal correction and integration of data from multiple analytical batches are also described.

http://dbkweb.mib.man.ac.uk/pubs/pdfs/Dunn-NatProt2011.pdf

Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry

Food allergy can result in considerable morbidity, impact negatively on quality of life, and prove costly in terms of medical care. These guidelines have been prepared by the European Academy of Allergy and Clinical Immunology's (EAACI) Guidelines for Food Allergy and Anaphylaxis Group, building on previous EAACI position papers on adverse reaction to foods and three recent systematic reviews on the epidemiology, diagnosis, and management of food allergy, and provide evidence-based recommendations for the diagnosis and management of food allergy. While the primary audience is allergists, this document is relevant for all other healthcare professionals, including primary care physicians, and pediatric and adult specialists, dieticians, pharmacists and paramedics. Our current understanding of the manifestations of food allergy, the role of diagnostic tests, and the effective management of patients of all ages with food allergy is presented. The acute management of non-life-threatening reactions is covered in these guidelines, but for guidance on the emergency management of anaphylaxis, readers are referred to the related EAACI Anaphylaxis Guidelines.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/all.12429

EAACI Food Allergy and Anaphylaxis Guidelines: diagnosis and management of food allergy

The study of biological systems in a holistic manner (systems biology) is increasingly being viewed as a necessity to provide qualitative and quantitative descriptions of the emergent properties of the complete system. Systems biology performs studies focussed on the complex interactions of system components; emphasising the whole system rather than the individual parts. Many perturbations to mammalian systems (diet, disease, drugs) are multi-factorial and the study of small parts of the system is insufficient to understand the complete phenotypic changes induced. Metabolomics is one functional level tool being employed to investigate the complex interactions of metabolites with other metabolites (metabolism) but also the regulatory role metabolites provide through interaction with genes, transcripts and proteins (e.g. allosteric regulation). Technological developments are the driving force behind advances in scientific knowledge. Recent advances in the two analytical platforms of mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy have driven forward the discipline of metabolomics. In this critical review, an introduction to metabolites, metabolomes, metabolomics and the role of MS and NMR spectroscopy will be provided. The applications of metabolomics in mammalian systems biology for the study of the health–disease continuum, drug efficacy and toxicity and dietary effects on mammalian health will be reviewed. The current limitations and future goals of metabolomics in systems biology will also be discussed (374 references).

Systems level studies of mammalian metabolomes: the roles of mass spectrometry and nuclear magnetic resonance spectroscopy

in Mass Spectrometry-Based Metabolomics and Lipidomics Tomas Cajka† and Oliver Fiehn*,†,‡ †UC Davis Genome Center−Metabolomics, University of California Davis, 451 Health Sciences Drive, Davis, California 95616, United States ‡King Abdulaziz University, Faculty of Science, Biochemistry Department, P.O. Box 80203, Jeddah 21589, Saudi Arabia ■ CONTENTS Sample Extraction 525 Extraction of Polar Metabolites (Metabolomics) 525 Extraction of Lipids (Lipidomics) 527 Combined Extraction of Amphiphilic and Lipophilic Metabolites 527 Mass Spectrometry-Based Metabolomics and Lipidomics 528 Direct Infusion MS 528 Ion Mobility-Mass Spectrometry (IM-MS) 529 Liquid Chromatography−Mass Spectrometry (LC−MS) 533 Reversed-Phase Liquid Chromatography (RPLC) 533 Hydrophilic Interaction Chromatography (HILIC) 534 Normal-Phase Liquid Chromatography (NPLC) 535 Supercritical Fluid Chromatography (SFC) 535 Two-Dimensional Liquid Chromatography (2D-LC) 535 Mass Spectrometric Detection 536 Data Processing 540 Quality Control 541 Conclusions 541 Author Information 542 Corresponding Author 542 Notes 542 Biographies 542 Acknowledgments 542 References 542

Toward Merging Untargeted and Targeted Methods in Mass Spectrometry-Based Metabolomics and Lipidomics.

Advanced glycation endproducts in food and their effects on health.

The following study investigates the preparation of human blood plasma for metabolomic profiling analysis by ultrahigh performance liquid chromatography coupled to time-of-flight mass spectrometry (UPLC/TOFMS) in a novel two-step design study. Four different organic solvents (acetonitrile, acetone, methanol, and ethanol) were used to assess human blood plasma preparation via protein precipitation. The optimal conditions for sample preparation were investigated, with consideration to the number of extracted markers, data quality/reproducibility, and column lifetime prolongation. Isotopically labeled internal standards were used to monitor data quality/reproducibility. Gel electrophoresis was also used to measure the protein content in the supernatant of the "first design step" allowing assessment of the amount of protein that would be injected/accumulate onto the column after many injections that would be apparent in a global metabolic profiling study. The second design step followed on from the results obtained in step one, with four of the best conditions selected and further investigated, looking at the effects of vortex time and temperature on precipitation/extraction. Two choices of solvent compositions were found to be "optimal" for preparation of plasma for global metabolic profiling analysis; these were "methanol/ethanol" (1:1, v/v) and "methanol/acetonitrile/acetone" (1:1:1, v/v/v) added to plasma (4:1 ratio, 400 microL total volume).

Investigation of Human Blood Plasma Sample Preparation for Performing Metabolomics Using Ultrahigh Performance Liquid Chromatography/Mass Spectrometry

A method is described for the analysis of the 16 polycyclic aromatic hydrocarbons (PAHs) prioritized by the USA EPA in meat sausages grilled under common barbecue practices. Quantification was done by GC−MS using perdeuterated internal standards (IS). Validation was done by spiking the matrix at the 0.5 and 1.0 μg/kg levels. The average of expected values ranged from 60 to 134% (median 84%) at the 0.5 μg/kg level and from 69 to 121% (median 96%) at the 1.0 μg/kg level. The median of the limits of detection and quantification were 0.06 and 0.20 μg/kg, respectively, for a 4-g test portion. The carcinogenic PAHs were below the quantification limit in all products except one lamb sausage. Comparison of estimates when either 1, 5, or 16 perdeuterated PAHs were used as IS showed that the most accurate determination of PAHs required that each compound be quantified against its corresponding perdeuterated analogue. Keywords: Polycyclic aromatic hydrocarbons (PAHs); meat sausage; gas chromatography−mass spectromet...

Quantitative determination of polycyclic aromatic hydrocarbons in barbecued meat sausages by gas chromatography coupled to mass spectrometry.

Modifications of milk constituents during processing: A preliminary benchmarking study

Determination of the antibiotic chloramphenicol in meat and seafood products by liquid chromatography-electrospray ionization tandem mass spectrometry.

Corn-based food and feed products purchased in Switzerland were analyzed for fumonisin B 1 (FB 1 ) and fumonisin B 2 (FB 2 ) using high-performance liquid chromatography. Forty-four samples (36.7%) of 120 were found positive for FB 1 (55-790 ng/g), with only 15 containing detectable levels of FB 2 (50-160 ng/g). The highest frequency of positive samples and also the highest FB 1 concentrations were found in corn grits (61.8%, 790 ng/g), followed by corn-based poultry feed (27.3%, 480 ng/g)

Véronique Parisod

Papers

Investigation of Human Blood Plasma Sample Preparation for Performing Metabolomics Using Ultrahigh Performance Liquid Chromatography/Mass Spectrometry

Quantitative determination of polycyclic aromatic hydrocarbons in barbecued meat sausages by gas chromatography coupled to mass spectrometry.

Modifications of milk constituents during processing: A preliminary benchmarking study

Determination of the antibiotic chloramphenicol in meat and seafood products by liquid chromatography-electrospray ionization tandem mass spectrometry.

Occurrence of fumonisins B1 and B2 in corn-based products from the Swiss market