I am using galaxy W4M server to process a set of lipidomics data (.raw files) that was converted to mzXML files using msConvert and in these mzXML files, I can see several peaks ranging from 67-2300 m/z, which corresponds to our acquisition m/z range and method run time of 17 mins. The files were uploaded individually (131 files) and under the “xcms plot chromatogram” module, the TIC chromatograms showed peaks along the run time of >1000 seconds (or ~17 mins). However, as I progressed to the “xcms findChromPeaks merger” module to merge the individual extracted files, there is a peak density pdf output and I can see two problems: i) the retention time was cut off at ~250 seconds (4.2 min) and ii) m/z was cut off at 996.6586. It seems that there is a problem in xmcs reading the msconverted files? We also encountered the same problem in the xcms .r package. I was wondering if other users have encountered such a problem, and how we may be able to resolve this issue?