Dear RG Community,
I am currently trying to handle CDF files in R (xcms package). These files contain information that was yielded from a GCMS analysis. I start to understand that the Gaschromatography part outputs spectra (Signal Intensity vs Retention Time(Rt)). Then, the Massspectrometry seems to look at GC signals in finer detail and splits them up by their mass to charge (m/z) ratio, correct?
The xcms package seems to handle the CDF file just fine. However, I feel a bit lost when trying to understand how to handle/analyse the spectra. My first intention is to convert the Rt, m/z and the intensities into a single matrix/dataframe to apply alignment/normalization methods on it. But the total amount of spectra that come from a single CDF file is somewhat overwhelming.
Could you recommend good resources that help me to understand GCMS objects? I already did the standard google research but was not able to draw many conclusions from it.
Thanks!
Rene
The netCDF format for GCMS is also known as ANDI (Analytical Data Interchange Format, AIA and perhaps some other names. The format is specified in the ASTM E1947 Standard. The data for GCMS is a three dimensional data format, with a retention time, and its correlated m/z value and amplitude. If you are looking to occasionally do additional processing, there are packages which will transform the data into CSV like text files which can then be read into most data analysis and presentation software. Functionally, GC/MS data is a data table of amplitude versus scan time and mass to charge ratio. OpenChrom is a free package which has a number of formats which can be imported and exported. GC and GC/MS file translator Pro is a commercial software that also does a lot of different file translations. Your GC/MS software package may also have the option to exprot the data into a format that you can deal with more easily.
Frankly, it would likely be easier to find a software package that will do the processing that you want to do, rather than writing our own. There are a huge number of software packages out there that do most of the things that would make sense to do with the data.
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