I am looking for ways to convert a Thermo Xcalibur RAW file to DTAs and/or MGFs in such a way that useful attributes, for example the relative time the sample was taken, are preserved in headers or by encoding into the file name. I would like to automate the conversion as much as possible.

It looks like Mascot could do this from Mascot Daemon provided we purchase the Mascot Toolbox:
http://www.matrixscience.com/help/instruments_xcalibur.html
We would have to convert to MGF to get the sample times. Has anyone tried this, and how did it work out?

Given the existence of the Thermo MSFileReader, it may be easier to just expand this perl module to do what we need:
http://sjsupport.thermofinnigan.com/public/detail.asp?id=586
Has anyone run this module against MSFileReader instead of the XDK? How did that work out?

If there is no better alternative, I may write a converter to add to this module and/or use this module. Would anyone be interested in using and helping to debug/maintain such a module?

Best Regards,

Peter H. Smith
phs at med unc edu