Fig 1.
Schematic depiction of iMet-Q workflow for peak detection and peak alignment.
Fig 2.
A cartoon for the illustration of constructing extracted ion chromatograms.
The blue straight lines represent the clustered signals, w and t are the FWHM and retention time of , respectively. Signal A and B are determined as the boundaries of the EIC, and the area in light blue color is the abundance.
Table 1.
The quantitation error (%) of seven standard metabolites calculated by iMet-Q, XCMS, MetAlign, and MZmine 2.
Table 2.
The reproducibility (Rep.) and normalized abundance (Abund.) of two internal standards detected by four quantitation tools.
Fig 3.
The box plot of abundance correlation of 167 elucidated metabolites across replicates in the public Arabidopsis data detected by the four quantitation tools.
Fig 4.
Hierarchical clustering by using the quantitation results of iMet-Q, XCMS, MetAlign, and MZmine 2.
Each entry in the tree leaves of a dendrogram represents a replicate. For each tool, we first combined its quantitation results of positive- and negative-ion modes. Colors were assigned to each replicate in the combined quantitation results according to the plant classes which the replicates originated from as follows: orange for cotyledon, red for stem, green for leaf, blue for flower, light blue for shoot apex, yellow for root, pink for seed, and gray for silique. Next, the figure was produced using MATLAB dendrogram function with PMMCC as the abundance correlation measure between any two replicates in the combined quantitation results.
Fig 5.
The box plot of abundance correlations between 19 verified metabolites and their in-source fragments detected in the public Arabidopsis data.
Fig 6.
The main graphical user interface of Metab-Q.
The Arabidopsis data from positive-ion mode is used as an example. After processing the data, Metab-Q lists the detected peaks in the summary table where the peaks are sorted according to their retention time. When users select peaks of interest in the summary table, the abundances of the selected peaks in different samples are plotted in the sample abundance plot and the detailed information of the selected peak in the technical replicates of a sample is listed in the panel below the summary table. The left panel is the quantitation parameter explorer that lists the parameters of a quantitation. Users can use the provided filter function to narrow down the number of peaks in the summary table.