LCMS data export to Matlab

[guira]

Hi all

I'm using a Waters UPLC-Synapt system. This system is used everyday for metabolomic studies. In spite of that I can't find the way to export MS chromatograms as .txt,.csv, .mat,... files.
Is there a 'usual' way to export raw data to be used in Matlab?
thanks in advance
G.

[lmh]

I'm not really qualified to comment, being a Thermo/Agilent user, but for information: we export into either cdf or mzXML (preferably mzXML). The transproteomic pipeline site:
http://tools.proteomecenter.org/wiki/in ... mats:mzXML
has a list of software that can do this.
The bioinformaticists with whom I have best links don't use the data directly in Matlab, but first process it to a peak list in xcms, and then import the peaklist into Matlab for PLS-DA and other typical metabolomic analyses. I don't know what other groups do.