Skip to main content
Topic: MS-DIAL 4.60 was released. (Read 533 times) previous topic - next topic

MS-DIAL 4.60 was released.

Dear users,

I uploaded the latest version of MS-DIAL environment today.

Below is the summary of this update.

The MS raw data of SCIEX (.wiff, .wiff2), Thermo (.raw). Agilent (.d), and Waters (.raw) can be imported directly without any data conversion.
SWATH-MS type acquisition in SCIEX WIFF1/WIFF2 and Thermo RAW was validated.
AIF type acquisition in Agilent data was validated (The abf file format for Waters MSE is still needed. However, it will be fixed soon).
Raw data of Agilent and Waters can be imported by "drag and drop" of the analysis files in the analysis file import window.
The option "N% detected in at least one group" was added to GCMS project.
SIRIUS .ms format was supported as a peak list export option.
The peak picking algorithm was improved (see
Lipidomics platform (including MS/MS search function) was improved.
The function of "gap filling by compulsion" was fixed (see


Hiroshi Tsugawa

Re: MS-DIAL 4.60 was released.

Reply #1
Dear Hiroshi,
Thank you very much for this software and your investment in improving the software.
I downloaded the new version of Ms Dial (4.60).
When I open an MsDial and fill in my working folder and want to continue I get this error message. Have you ever encountered this problem?

Best regards


Re: MS-DIAL 4.60 was released.

Reply #2
Hello Hiroshi,

I receive the same error as Sebas when attempting to open the IM-MS/MS tutorial data in the 4.60 version. I attached the picture for clarity.

In attempts to resolve, I did the following:
 - downloaded the lmb2 file from the MSDial website and moved the file into both the data folder and the program folder
- downloaded the lmb file from the MSDial website and moved the file into both the data folder and the program folder

Neither resolved the issue. However, the data opens perfectly fine in 4.48.

Thank you,

Re: MS-DIAL 4.60 was released.

Reply #3
Dear users,

sorry for this issue. It is because that two lbm2 files are contained in the same ms-dial folder.
I just forgot to delete one of them...I reuploaded the same ms-dial kit containing only the latest library file (lbm2).


Re: MS-DIAL 4.60 was released.

Reply #4

This is a stupid question (sorry to ask) but there is a MSDIAL.exe file to start the program when you download the Window version for Window but for the Mac version in the downloaded folder which file start start the program (yes I'm blocked at this step= start the GUI program)?
Thanks for your help

Re: MS-DIAL 4.60 was released.

Reply #5
Thx Hiroshi for your great work!

So far everything works fine. Checking some of my steroid test datasets with recent in-house DB version and realized one thing - it would be great to have a separate functionality for postIdent, which allows for a choice of postIdent list entry for the annotated feature (similarly to Compound search for MS2 annotation).

Sometimes comes a situation, where two closely eluting isobaric compounds are annotated with the same record, because it's eluted slightly closer and gained higher score. For now it's a tedious process of manually opening the list, sorting on RT and looking what could be nearby.

Re: MS-DIAL 4.60 was released.

Reply #6
I tried installing MSdial 4.60 on my mac, but the zip file doesn't seem to contain an executable file. I think this is the same problem as cduplais described above? Maybe I'm missing something?

Thank you,

Re: MS-DIAL 4.60 was released.

Reply #7
Dear Kyra and all,
as I noticed at the previous update, the msdial in mac/linux is currently available as the command line application. If you use the GUI app, you have to use Windows OS. You can run the msdial console app of mac/linux with the "-p" option that creates the project folder which can be opened in the Windows GUI application.

And Sergey,

thanks for the suggestions. I also recently think the same demand in my private research. I will create the functionality in the next update.


Re: MS-DIAL 4.60 was released.

Reply #8
Dear users,

also make sure, the direct import for MS raw data is only available in Windows GUI application.
This is because the API for reading MS data was built in .net framework environment (you do not have to understand this) in the MS vender's side. In future, it may be improved to be used in any type of OS.
Also, although I wrote the parser of Bruker's MS data, I recommend to convert Bruker's .d file into abf (for normal LC-MS) or ibf (for ion mobility data) for the rapid data retrieving in MS-DIAL application at this moment.




Re: MS-DIAL 4.60 was released.

Reply #9
Dear Hiroshi,

Many thanks for releasing such a great software. I could successfully load and process my wiff2 files acquired in IDA mode.  Then I also tried with wiff2 acquired in SWATH mode, but MS -DIAL does not seem to be able to load MS2 correctly. The shape of MS1 TIC is also sawtooth, so something seems wrong. You mentioned that SWATH-MS has been validated, but has SWATH-MS with WIFF2 also been officially validated to work?

Thank you,


Re: MS-DIAL 4.60 was released.

Reply #10

could you please send me one of your wiff2 file?Actually, I validated the function by using wiff2 that I have. But I have little experience personally for using the wiff2 format file. Therefore, your help is very welcomed to improve my program's robustness. Thanks,