Dear Ralf,
Cody in our lab introduced me to XCMS. Cody uses it for alignment of LC/MS data. I would like to find out whether XCMS can be used to align MS spectra from multiple replicates of laser desorption experiments. We are planning metabolic profiling of mouse serum by laser desorption.
Thanks. Michal
It is supported by the XCMS R package (e.g. alignment described here http://bioconductor.org/packages/2.10/b ... Direct.pdf (http://bioconductor.org/packages/2.10/bioc/vignettes/xcms/inst/doc/xcmsDirect.pdf))
but we do not support it through the XCMS Online interface at the moment.
The reason is that parameter optimization (feature detection, alignment) for that type of data is more complicated.