Aglient MassHunter file exportation to metAlign
Posted: Tue Sep 25, 2018 4:17 pm
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:
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?
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?