MetAlyzer User Guide

Nils Mechtel, Carolin Andresen & Luis Herfurth


The package provides methods to read output files from the MetIDQ™ software into R. Metabolomics data is read and reformatted into an S4 object for convenient data handling, statistics and downstream analysis.


There is a version available on CRAN.


The latest version can directly be installed from the github.



The package takes metabolomic measurements as “.xlsx” files generated from the MetIDQ™ software. Additionally, meta data for each sample can be provided for further analysis.

Effective quantification of metabolites requires a reliable signal. The limit of detection (LOD) is defined as 3 times signal-to-noise of the baseline, calculated by the software MetIDQ™ for each metabolite. Values are classified as “Valid”, “LOQ” (below limit of quantification) or “LOD” (below limit of detection). This information is encoded in the color in the “.xlsx” table. Further color codes can include “ISTD Out of Range”, “Invalid” and “Incomplete”. The MetAlyzer packages allow to read both information, the value and the quantification status, gives statistics about the quantification efficacy and allows filtering based on the LOD.