- Referenced WorkFlows and Histories
- How to contribute?
Raw data pre-processing with XCMS
XCMS is a free software dedicated to pre-processing any types of mass spectrometry acquisition files from low to high resolution including FT-MS data coupled with different kind of chromatography (liquid or gaz). This software is used worldwide by a majority of specialists of metabolomic using mass spectrometry methods.
This software is based on different algorithms that have been published and is maintained on the R repository [5,6,7].
XCMS is able to read files with open format as mzXML and netCDF which are independent of the constructors' formats.
It is composed of R functions able to extract, filter, align, fill gap and annotate isotopes, adducts and fragments. This set of functions gives a modularity particularly well adapted to defined workflows which is one of the key points of Galaxy (Figure 4).
Figure 4: The original XCMS worflow and its implementation within W4W.