Hi,
I am new to XCMS online. I am trying to setup parameters to analyse some direct infusion orbitrap data. When I try and edit a parameter set the only options available to me in the dropdown are matched filter and centWave, both of which are for LC data and predictably do not find any features in my data.
How do I access the MSW function, which I think is the one I want for peak detection for infusion data? Also any other tips people have for this kind of analysis would be much appreciated, I normally use LC-MS.
cheers
Russ
"MSW" is not available as a processing method in XCMS Online at the moment.
The reason is that MSW has a lot of parameters that need to be optimized according to your data.
Therefore it is much harder to create "default" parameter sets for DIMS data. The result will likely be disappointing without an initial systematic parameter optimization.
However, you can apply this method using the XCMS R package as described in the documentation. (http://http://bioconductor.org/packages/2.11/bioc/vignettes/xcms/inst/doc/xcmsDirect.pdf)
Looking at the original MSW publication might help to optimize the parameters.
Du, P., Kibbe, W.A. and Lin, S.M. (2006) Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching, Bioinformatics, 22, 2059-2065.