Software for deconvolution of NPLC-APCI-MS chromatograms

[NicholasD]

Hello all, I am faced with the following challenge:

I need to be able to (quickly but sufficiently accurately) map and at least relatively quantify changes between various samples of non-polar hydrocarbon mixtures.
I'm using an NPLC routine for rough separation, and can do online APCI-Orbitrap MS. I would like to use something akin to a Kendrick plot for characterisation, but in 3D, and with integrated abundances for individual masses on the z-axis. Due to the large numbers of compounds in the mix this is impossible to do manually. I've tried deconvoluting with Mass Frontier, but either I'm doing it wrong, or it simply can't identify the right masses as "compounds", as it always assumes fragmentation, which APCI doesn't do. I need to be able to have one main m/z per compound (with M+ and M+1 base mass peaks + isotopes).

Does anyone know of a software that could achieve such a feat? Essentially automatically integrating extracted ion chromatograms for a large number of m/z ranges - at best auto-picking the right ranges, too, of course!

Thanks a lot for any help!

[lmh]

If you're aiming to look for differences in peak-areas between two (or more) types of samples, and you want to do so by looking at any peak in the sample without preconceptions of what might be there, you could consider XCMS (but there are other solutions out there).
XCMS is free, open-source software running in R, and will slice the data into a huge number of extracted ion chromatograms, searching each for peaks. It will tabulate all the peaks it finds, and given multiple samples, it will work out which peak in sample 1 corresponds to which in sample 2 (etc.) allowing for minor variations in mass, and retention-drift. It can tabulate the peaks in all the samples (and also do t-tests between two treatments if you've only got two; otherwise you can analyse the table however you want).
It does have an annotation add-on, so far as I know (called CAMERA) which will attempt to weed out the obvious related ions (H+ and Na+ adducts, isotope peaks, etc.).
Since it's open-source it's not tied to any particular manufacturer and doesn't read Thermo's raw data format. You'll need to convert to mzXML or similar. There are various third-party file converters available, but they'll probably have to run on a PC that has Xcalibur loaded as they rely on things that Thermo export.

[NicholasD]

XCMS

That's great, thanks, that sounds like just what I'm looking for!