The Sequenom iPlex MassArray system uses MALDI-TOF mass spectroscopy to measure genotypes. A multiplex-PCR is used to assay up to 40 loci simultaneously.
I've got some iPlex .xml files that are compatible with the Sequenom Typer analysis software, but I'm finding it difficult to use Typer for my analysis, so I'm trying to parse the .xml files directly in R.
Most of the XML elements are straightforward, except for the "spectrum" element. Each spectrum is a comma-delimited vector of double-precision floating point numbers like:
<spectrum pk="771240" well-pk="903654" well position="P24">2.018000e+003,1.000000e+000,1.004800e+004,3.775512e+003...</spectrum>
I've used the R "XML" package to extract the vector and plot it, and it looks very different from the spectra when viewed in Typer.
Has anyone else tried doing this? I'm sort of thinking that they may be using some sort of Fourier transform or spectral analysis to transform the spectrum, but I haven't been able to find any documentation on it.