Galaxy wrapper for Isotopologue Parameter Optimization (A Tool for automated Optimization of XCMS Parameters)
Peak picking parameters optimization by using natural, stable 13C isotopic peaks to calculate a peak picking score.
IPO optimizes XCMS peak picking parameters by using natural, stable 13C isotopic peaks to calculate a peak picking score. Retention time correction is optimized by minimizing relative retention time differences within peak groups. Grouping parameters are optimized by maximizing the number of peak groups that show one peak from each injection of a pooled sample. The different parameter settings are achieved by design of experiments, and the resulting scores are evaluated using response surface models. IPO was tested on three different data sets, each consisting of a training set and test set. IPO resulted in an increase of reliable groups (146% - 361%), a decrease of non-reliable groups (3% - 8%) and a decrease of the retention time deviation to one third.
Link to the publication - http://www.biomedcentral.com/1471-2105/16/118
The tool requires CDF files as input (can be extended to other file formats as well) and performs the XCMS optimisation. Output is a html file with the graphs, links to the CSV (results) and log files.comments powered by Disqus