Proteowizard converts .raw files to mzXML/mzML but it does not calibrate the data at the moment.
One way is to export the (calibrated) data into CDF files using MassLynx.
However, if you need to convert to mzXML then you can use a workaround that is shown here (http://http://metabolomics-forum.com/viewtopic.php?f=8&t=352).
I made an R package that contains a function to convert waters files correctly. It is using masswolf and hence Masslynx needs to be installed. It should work correctly for MSn (converting to netCDF makes the data appear like MS1 data) and it makes separate files for MSE runs.
Note that it has only been tested with a limited number of instruments and Waters sometimes change the format slightly so the converted files should be compared to the data as shown by Masslynx.
EDIT: LINK!: https://github.com/stanstrup/chemhelper (https://github.com/stanstrup/chemhelper)
EDIT: moved here https://github.com/stanstrup/convert.waters.raw (https://github.com/stanstrup/convert.waters.raw)
Jan,
can you provide a link to your R package ?
Added. I have made it a rule to never miss a chance to look distrait.
Great, thanks for sharing !
I have Waters raw folders that I converted to mzXML using Proteowizard. Viewing the files in Insilicos Viewer and later trying to run XCMS, I noticed the scans were separated by the experimental and calibrant peaks. Is there a way to, without using MassLynx (since I have no way to get it), properly calibrate and convert the files?