MS-DIAL console application

Program download

The console application is stored in the same folder of MSDIAL GUI. MS-DIAL program.

See the main page too.

Demonstration files

All of demonstration files for GC/MS, LC-MS/MS (data dependent acquisition), and data independent MS/MS acquisition can be downloaded from here. MsdialConsoleApp demo files

Tutorial

This is a quick tutorial of MSDIAL console application. The main processer is stored in the same folder of MS-DIAL GUI program.

Just type MsdialConsoleApp.exe to show the help.


(Note 1) All of the results like feature detection, deconvolution, and alignment was stored in "*.msdial" ASCII format file. You can open it in Excel by drag-and-drop of the file.
(Note 2) If you want to keep MTD format file to be used in MS-DIAL GUI, type "-p" as an option like:
> MsdialConsoleApp.exe lcmsdda -i .\LCMS_DDA\ -o .\LCMS_DDA\ -m .\LCMS_DDA\Msdial-lcms-dda-Param.txt -p

1. GC-MS process


The program accepts netCDF, mzML, or ABF files.
The demonstration is just for a basic processing (just peak detection and alignment).
The result is written as the extension of "***.msdial" in the output directory.

(Note 1) If you want to calculate retention indexes, see FAMEs RT dictionary pathes.txt and FAMEs RT.txt in GCMS folder.
The parameter setting for RI calcuation is also written in Msdial-GCMS-Param.txt.

(Note 2) If you want to identify the targeted metabolites, this program accepts MSP format file.
The required field is also written in the parameter file.

(example)
> MsdialConsoleApp.exe gcms -i .\GCMS\ -o .\GCMS\ -m .\GCMS\Msdial-GCMS-Param.txt

*below is a quick explanation of how to set MSP file and RI index files.
The MSP setting is also the same in LCMS projects.



2. LC-MS or LC-MS/MS (data dependent acquisition)


The program accepts netCDF, mzML, and ABF files.
The result is written as the extension of "***.msdial" in the output directory.
Please type lcmsdda unless you process data independent acquisition data like SWATH.

(Note 1) If you want to identify the targeted metabolites, this program accepts MSP format file.
The required field is also written in the parameter file.

(example)
> MsdialConsoleApp.exe lcmsdda -i .\LCMS_DDA\ -o .\LCMS_DDA\ -m .\LCMS_DDA\Msdial-lcms-dda-Param.txt

3. LC-MS/MS (data independent acquisition)


The program accepts ABF format file only.
The DIA file path must be required. See the Msdial-lcms-dia-Param.txt and Plasma-HILIC-SWATH-Experiment.txt to check the detail. Also, see the main tutorial for futher detail.
The result is written as the extension of "***.msdial" in the output directory.
Please type lcmsdia for the processing.

(Note 1) If you want to identify the targeted metabolites, this program accepts MSP format file.
The required field is also written in the parameter file.

(example)
> MsdialConsoleApp.exe lcmsdia -i .\LCMS_DIA\ -o .\LCMS_DIA\ -m .\LCMS_DIA\Msdial-lcms-dia-Param.txt

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