Converting Waters .raw files to mzXML

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Converting Waters .raw files to mzXML

December 07, 2012, 11:26:02 AM

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.

Re: Converting Waters .raw files to mzXML

Reply #1 – April 03, 2014, 06:59:58 AM

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
EDIT: moved here https://github.com/stanstrup/convert.waters.raw

Re: Converting Waters .raw files to mzXML

Reply #2 – April 03, 2014, 09:25:31 AM

Jan,

can you provide a link to your R package ?

Re: Converting Waters .raw files to mzXML

Reply #3 – April 03, 2014, 09:31:26 AM

Added. I have made it a rule to never miss a chance to look distrait.

Re: Converting Waters .raw files to mzXML

Reply #4 – April 03, 2014, 11:56:37 AM

Great, thanks for sharing !

Re: Converting Waters .raw files to mzXML

Reply #5 – October 22, 2014, 05:57:29 PM

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?