Samples metabonomics experiments

When designing a metabonomic experiment it is critical to control as much as possible all the factors that affect the baseline of detected metabolites. These factors include but are not limited to species, strain, gender, diet, age, diurnal variation, changes in gut microflora, lifestyle, and time of sampling [34,50,77-82],... 

In a GC-MS or LC-MS metabonomics experiment each file represents a single biological sample. The basic goal of data processing is to transform raw data files to a standard and uniform format so that statistical analyses can be carried out. A variety of instrument vendors utilize different proprietary data formats. Thus, the first step in data processing requires a conversion of such raw proprietary data into common raw data format such as ASCII text or binary netCDF. More recently, a universal mzXML format has become more popular. Many vendor instrument software packages contain scripts to allow for such a file conversion [76],... 

Designing a successful metabonomics experiment is truly a multidisciplinary exercise, and one must consider details of the in-life portion, sample collection, sample preparation, analytical data generation, data processing, analysis, and interpretation. The in-life portion involves study subjects selection, acclimatization, dosing or treatment, and sample collection and has been discussed in detail elsewhere (Robertson et al., 2002). The following sections will focus on the remaining steps in this process as it pertains to LC—MS. 

Sample preparation is one of the most critical steps in a successful metabonomic analysis. The composition of any biological (plasma, urine, bile) or an in vitro sample is very complex, and the quantity of metabolites detected depends to a large extent on how the sample is prepared for analysis. In a nontargeted metabolomics experiment, the purpose of sample preparation is to remove any large molecules (proteins, peptides) and salts, while retaining a wide range of small molecule metabolites. The more steps in sample preparation, the narrower will be the chemical diversity of compounds present in the final sample [90],... 

One of the most commonly encountered questions is "How long do I have to wait until my sample reaches equilibrium " This is just as important for high throughput studies such as metabonomics and medical diagnostics that use only a few scans as it is for multidimensional biomolecular studies where a single experiment can last up to 6 days. The answer (and solvent suppression method) depends on the application. 

NMR spectra were recorded as ID H NMR experiments using a N OESY water suppression sequence with experimental parameters optimized for urine samples in the field of metabonomics. Mass spectra were acquired by... 

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