Therefore, AMDIS data requires manual inspection to define the correct metabolite to be assigned to each retention time. Finally, according to the configurations used when applying AMDIS, it may report more than one metabolite identified for the same retention time. However, AMDIS may use different ion mass fragments for quantifying the same metabolite across samples, which indicates that using AMDIS results one is not comparing the same variable across experimental conditions. As the area of a peak may be influenced by coelution of different metabolites, the abundance of the most abundant ion mass fragment is commonly used for quantifying metabolites in biological samples. It quantifies metabolites by calculating the area (Area) under their respective peaks or by calculating the abundance of the ion mass fragment (Base.Peak) used as model to deconvolute the peak associated with each specific metabolite. In addition, AMDIS shows some limitations when quantifying metabolites. However, this report contains the results of samples placed on top of each other, which also requires extensive manual process before statistical analysis. AMDIS also allows users to generate a single report containing the results for a batch of samples. First, it generates results in a single spreadsheet per sample, which means that one must manually merge the results provided by AMDIS in a unique spreadsheet for performing further comparisons and statistical analysis, for example, comparing the abundances of metabolites across experimental conditions. Although AMDIS is widely and successfully applied to chemistry and many other fields, it shows some limitations when applied to biological studies. It is execellent in deconvoluting chromatograms and identifying metabolites based on a spectral library, which is a list of metabolites with their respective mass spectrum and their associated retention times. AMDIS is one of the most used software for deconvoluting and identifying metabolites analysed by Gas Chromatography - Mass Spectrometry (GC-MS). Metab is an R package for processing metabolomics data previously analysed by the Automated Mass Spectral Deconvolution and Identification System (AMDIS) (). See data(exampleMetReport) to see an example of the data frame produced by MetReport.Note that the first line of the resulting ame is used to represent sample meta-data (for example replicates). MetReport generates a data frame containing the metabolites identified in each biological sample and their respective abundancies/intensities.
A character vector indicating the path to the folder where the results must be saved, if save = TRUE.
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