Aglient MassHunter file exportation to metAlign

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4 posts Page 1 of 1
I'm testing a scheme for untargeted analysis of GC-MS data acquired with Agilent MassHunter: using metAlign for baseline correction (no alignment) and then switching over to OpenChrom for AMDIS deconvolution and NIST library identification.

I have attempted to export the .D data from MassHunter Qual (B.07.00 SP2) as the mzData format, but when I look closer it is file type .mzdata.xml, which metAlign won't recognize.

So, I thought I used mzMine 2 to open the .mzdata.xml file and export as .cdf. metAlign sees this just fine but when I try to do baseline correct it seems to hang up.

I have one data file that I somehow transformed "correctly" because metAlign works on it and produces the reduced data. However, I tried the above process again (MassHunter export to mzdata.xml; mzMine export to .cdf) with the same .D file and metAlign hangs up until I Ctrl+C out of the terminal window.

Last line in the terminal is below:

Code: Select all

C:\[directory for metAlign]>jdx2netcdf "C:\[directory for metAlign]\Output1\TEMP.JDX" 1.000000
jdx2netcdf C:\[directory for metAlign]\Output1\TEMP.JDX 1 --> C:\[directory for metAlign]\Output1\TEMP.cdf

I don't know how I got a .cdf that works yesterday, but my .cdf now don't.
I guess a problem is happening with the jdx2netcdf application?

Any suggestions?
Caitlin Swanson
Volatile Analysis Corporation
So I didn't find out why my original export didn't work, but I did find a tool called ProteoWizard (, which has a nifty program called MSConvert that will allow you to read Agilent MassHunter GC data files (.D) and convert them to the .mzXML format, which is readable by MetAlign.

MSConvert does not seem to recognize the older ChemStation .D format, but if you have the translator that comes with the MassHunter software you can make the ChemStation data readable by MassHunter programs.
Caitlin Swanson
Volatile Analysis Corporation
./ucc outdata.cdf
./ucc msdata.MSScan.bin outdata.cdf
Thank you for the alternative. I was able to convert a Chemstation .ms file, but the MassHunter msscan.bin file I haven't been able to convert. Also, when I compare the .cdf generated by UCC the top part of my peaks seem to be cut off?
(Tried to insert an image, but it didn't seem to be working...)

.cdf, in blue, compared to same file as .mzXML, red, in MZMine
Caitlin Swanson
Volatile Analysis Corporation
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