Interpret Spectrum From Sequenom Iplex Massarray Xml File

Question

[dfornika]

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.

Answer 1

[Henning]

Are you a MassArray User?

[dfornika]

I'm not sure exactly what you mean. My lab had some Sequenom genotyping done by a core facility. I was given a set of reports and .xml files. We bought the Typer software to view the .xml files, but all the reporting functions have been disabled, making it very difficult to export data from Typer.

[Neilfws]

This is a question, not an answer. Please use comments under original question for these discussions.

Answer 2

[Swbarnes2]

Is there a reason you don't have the raw genotypes? I don't think that file is meant to be read by anyone but the Typer software.

[dfornika]

I have a set of reports and the .xml file, but I've been unable to export data from Typer in any useful way.

I'd like to be able to access my data transparently from the .xml files, since I've found Typer to be ill-equipped for data export.

[dfornika]

I have a set of reports and the .xml file, but I've been unable to export data from Typer in any useful way. I'd like to be able to access my data transparently from the .xml files, since I've found Typer to be ill-equipped for data export.

I agree that the file is not 'meant' to be read independently from Typer, but it's a plain-text XML file, there is plenty of data that can be gleaned from it. I'm just having trouble guessing the function that translates the vector of floating-point numbers in the .xml file to the spectrum that I see on a Typer screen.

[Neilfws]

Again, this is more a question than an answer. Please use comments under original question for these discussions.