Topic: opening agilent masshunter .xml files

so far i have had no success opening masshunter .xml files. I know mzdata files can be opened by mmass, but i would rather prefer to use the .xml variant as all the data points seem to be conserved in this format.

the file format looks pretty straight forward. If it is not to much of an effort, I would really appreciate if this could be integrated.

example file:

<?xml version="1.0" encoding="utf-16"?>
   <ReportTitle>MS Spectrum Results</ReportTitle>
      <Title>+ESI Scan (0.141-0.534 min, 25 scans) Frag=350.0V jf389 48h0003.d </Title>     
      <d i="0" x="100.0065" y="7.52" />
      <d i="1" x="100.0180" y="7.52" />
      <d i="2" x="100.0294" y="4.80" />
      <d i="3" x="100.0408" y="5.96" />
      <d i="4" x="100.0523" y="4.88" />
      <d i="5" x="100.0637" y="3.68" />
      more datapoints here

      <d i="78288" x="2998.4053" y="7.28" />
      <d i="78289" x="2998.4679" y="4.28" />
      <d i="78290" x="2998.5305" y="3.52" />
      <d i="78291" x="2998.5931" y="5.16" />
      <d i="78292" x="2998.6557" y="4.76" />


Re: opening agilent masshunter .xml files

what's wrong with mzData? All the data points should be there as well.


Re: opening agilent masshunter .xml files

Maybe I am mistaken or doing something wrong, but the file mzdata.xml file is a lot smaller, and when imported into mMass the signals are plotted as a single line for each mass (centroids?). So in the end experimental spectra look like they were calculated and the other way around.


Re: opening agilent masshunter .xml files

This is not a problem of mzData format. This is a problem of what type of data are exported from your raw file. You should be able to select either profile or centroids (continuous or discrete). Some of the software also enable direct copying of raw data into clipboard, which can later be imported into mMass right from the clipboard.


Re: opening agilent masshunter .xml files

you are right. found it now. in agilent masshunter indeed, there is an option to export profile instead of centroid data. although it is in a different menu (method explorer -> export), than the one i used for exporting. thanks for the hint.