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Messages - Hiroshi Tsugawa

MS-DIAL / Re: MS-DIAL for macbook with M1 chip
Dear Xiaohan

first of all, the GUI application of ms-dial is only available at Windows OS. The command line version is available at linux and mac. If you wanna use this as the command line application, please see below chats. (I attached the e-mail communication with a user)


Dear XXX,

Sorry for the late reply.

I did not get the same error in our environment, but I think the problem is probably the lack of a certificate.
The default macOS settings do not let you run applications without a certificate.

After discussing the issue, it was decided not to add a certificate, at least for a while. So we apologize for the inconvenience, but you will need to change your security settings if you want to use MSDIAL on macOS.

Please see this apple support page and try to change the settings. ( 
If this does not work, run the following command from Terminal.
>> sudo spctl --master-disable
Then, set the Security & Privacy, "Allow apps downloaded from" item in the System preference to "Anywhere".
You should now be able to run MSDIAL.

To restore the original settings, issue the following command.
>> sudo spctl --master-enable

If you still cannot run it, there is a problem other than the certificate. If this is the case, please contact us.

Thank you,

Dear YYY,

Thanks for getting back to me!

I tried to follow the tutorial and used the command you gave me, but there was another error that said libcoreclr.dylib is not valid. The full message that appeared in the command is as follow:

~MacBook-Pro MSDIAL ver.4.70 MacOS % ./MsdialConsoleApp

Failed to load a, error: dlopen(/Users/~/Downloads/MSDIAL ver.4.70 MacOS/libcoreclr.dylib, 1): no suitable image found.  Did find:

       /Users/~/Downloads/MSDIAL ver.4.70 MacOS/libcoreclr.dylib: code signature in (/Users/~/Downloads/MSDIAL ver.4.70 MacOS/libcoreclr.dylib) not valid for use in process using Library Validation: library load disallowed by system policy
Failed to bind to CoreCLR at '/Users/~/Downloads/MSDIAL ver.4.70 MacOS/'
Failed to create CoreCLR, HRESULT: 0x80008088

I would appreciate it if you would let me know how to solve this.


MS-DIAL / Re: MS-DIAL 4.70 and MS-FINDER 3.52 were released.
Thanks Sukis, I will check these soon.
Maybe, for the issue of agilent .d, the program cannot analyze the chemstation's .d file while it can process masshunter's .d file.
A best way is to use .netcdf format.

MS-DIAL / Re: Parameters and exports from MS-DIAL console application

by the command line application, right? Sorry, no. From the command line application, users cannot export the result by area instead of height...If you can write the source code, you can modify this by yourself because the source code is also available in my website.. From the next version, I will put such function to export the peak area in the command line tool.

MS-DIAL / MS-DIAL 4.70 and MS-FINDER 3.52 were released.
Dear users:

I officially released new versions of MS-DIAL and MS-FINDER as discussed in this forum.

Especially, below is the main functional updates.
1. Ready to directly import Bruker LC-MS (.d/.baf) and LC-IM-MS (.d/.tdf) data.
2. Command line function for LC-IM-DDA (like PASEF) and LC-IM-DIA (like diaPASEF and other AIFs) is now available (method "lcimdda" or "lcimdia").
3. Direct imports of Agilent, Thermo, Bruker, Waters, and Sciex were validated (by Drag and Drop).


Hiroshi Tsugawa

MS-DIAL / Re: MSDial Alignment Not Working
Sorry for the late reply, and actually I cannot answer to this issue because I cannot check your raw data.
Sometimes, it is due to that some of raw data are broken or coming from different ionization mode.
If you can finish processing by a part of data files and if you cannot finish processing by another part of data files, there is such a possibility. Also, you can simply check the file size for all the data, and if you find the one having really unexpected file size when compared with other files, try to process files without the file.

MS-DIAL / Re: How can I check MS1 isotopic pattern?
Dear Yunsun,

in the current ms-dial, you cannot find the exact isotopic pattern in the alignment result. Instead, you can check the isotopic pattern for each file's result. (go to the peak list export option)
Also, such a feature can be browsed in ms-finder program.

MS-DIAL / Re: question about QuantMass
Dear Isaac,

For the data comparison in the large scaled data set, we should keep the same quant mass value for metabolite quantification.
MS-DIAL offers such an environment.

(1) if you put "QUANTMASS: " field in your msp format file, the metabolite is always quantified by the target m/z.
(2) Go to "Quantmass browser" of "Post processing" in the msdial menu, then, you can define the m/z values for each metabolite.
The first option should be used if many biological samples are sequentially analyzed for a long time.