Closed joewandy closed 3 years ago
Looks like that might be hard to fix. Think kei might have found something similar and an older version of MSDIAL worked ok (I think the latest version just adds some ion mobility stuff that we’re not interested in)
We just need to make sure we’re using the version described in the CorrDecon paper
'Data were processed by MSDIAL version 4.12'
http://prime.psc.riken.jp/compms/msdial/download/repository/MSDIAL%20ver%204.12.zip
Will test later
Looks like you can drop back into v3.22 if necessary
v4.12 works on both the GUI and command line.
However it seems that from the terminal, the DIA mode only accepts input file in ABF format ..
(the DDA mode works with mzML files)
So we need to install ABF converter: https://www.reifycs.com/AbfConverter to get the DIA mzML files to this format. As a pre-requisite, this needs MSFile from thermo (install MSFileReader version 3.0 SP2 or higher except ver. 3.1 SP4).
I don't think converting from .raw is going to work. Remember that the RAW files had the apodization issue (peak smudging).
but looks like maybe that converter will convert from .mzML
Ignore the ABF stuff above. Version 4.12 works with mzML file from both the GUI and terminal (was mistakenly using an .mzXML file to test).
See:
For now, we ended up using two different versions of MSDIAL:
Have created a script msdial_wrapper.py
that can be used to launch MS-DIAL, either on a single mzML or a set of mzML files. However for multiple mzML, it seems tricky to enable CorrDec.
We can run MS-DIAL from the command line (refer to http://prime.psc.riken.jp/compms/msdial/consoleapp.html). Is it possible to script it for our experiments?
To test the console app:
MsdialConsoleApp.exe
program can be found in the same location as the GUI app.MsdialConsoleApp.bat
. This will run 3 example analysis: GC/MS, LC-MS/MS DDA, and LC-MS/MS DIA. Can ignore the GC/MS one.Msdial-lcms-dia-Param.txt
to adjust the path to the input DIA file in the LC-MS/MS DIA folder.Seems like some library loading / path problem? To check later..