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Messages - Hiroshi Tsugawa

MS-DIAL / Re: MS-DIAL 5 stability
Hi Ville

thanks for letting us know this issue. We will quickly check the second issue.
On the other hand, could you please let me know more details about the first thing?

Which ms-dial version did you use?
What type of data is imported?

MS-DIAL / VS4.9 and VS5-alpha series
Dear users,

Recently, I do not have much time to share my opinion/comment/suggestion to your posts.
I actually left RIKEN and started new career at tokyo university of agriculture and technology. In this year, I have to prepare many lecture slides for university's students...However, we are developing new ms-dial programs to boost metabolomics/lipidomics/proteomics studies. Here, I uploaded new programs.

Although we still take care about the current version 4 series for a while, our developers now focus on the development of new MS-DIAL 5 series. It can be download by ID and password until the publication, and please let me know if you have time to evaluate the program.

Hiroshi Tsugawa
MS-DIAL / Re: Retention times in MS-DIAL library.
Dear Ploutno

I simply integrated the individual MSP libraries to create the MSMS-Public-Neg-VS15.msp. I should note the origin of MSP database actually, but if you should know the origin, you should integrate each of MSP library by yourself to distinguish the origin of chromatography conditions.

MS-DIAL / Re: MS-DIAL 4.70 and MS-FINDER 3.52 were released.
Stefano-> I have already answered this question in the private chats. MS-DIAL can import the wiff2 data directly without conversion.
To all: sorry, the server will be rebooted on Nov. 8th. Thanks,


MS-DIAL / Re: MS-DIAL Alignment export result
Dear all,

below is the email communication.


see below? BTW, the sample data that you are trying to use is the data from our lipidomics experiment. Therefore, you should select "lipidomics" as the project information if you wanna see the full annotation performance of MS-DIAL program for the data.

1.       Why this metabolite is reported three times under different retention times (9.615min, 5.715min and 5.974min)?
-> When you do not use the retention time information, this situation will occur. That is, only using the MS/MS spectrum for annotation is not enough to distinguish isomers which have similar/same spectral patterns.

2.       Different area values are reported varying from 60 to 4199934. How I can interpret it?
->  Very small values like 80~500 can be interpreted as "noise level's peak". The peak was not be detected in the normal peak picking algorithm, but the peak information was inserted by the gap-filling algorithm.

3.       Reference RT is “null”. What does it mean?  In comparison for Naringenin (row 240) Relative RT value is 5.958min, while its Average RT is 1.379min. Shouldn’t it be very close?
-> The retention time information is not included in the reference msp file. Maybe, you did not use the retention time information for annotation (check the identification tab's parameter setting. You will see the check box like use retention time for filtering metabolites etc.)

4.       Fill%, which is equal to 0.091, 0.864 and 0.136 respectively. What is the meaning?

5.       Column P (RT matched) “TRUE” for all three cases. How it can be, taking into consideration the fact that RTs are very different?
The MSP file does not contain the suitable retention time information of metabolites for the "mouse tissue" data. Therefore, the retention time information of the msp file cannot be used for annotation actually.

6.       Manually modified for quantification “FALSE” – What does it mean?
In msdial, you can modify the peak picking result. If you modify, the case is changed to true.

7.       Total score with the value of about 85. What does it mean?
Max score will become 100. 85 would be a good score as the annotation criteria.

8.       Dot product and Reverse dot product. What is it?
See 20 page of

9.       Fragment presence % with value of 50 – What does it mean?
See 20-21 pages of

MS-DIAL / Re: MS DIAL - Scoring issues
Try to check the option of "Use RT for filtering candidates"  and "Use RT for scoring candidates". If you use these options, please check your RT tolerance setting. The total score calculated in the compound search windows does not consider the RT score, but in the data processing procedure, the RT score is also considered to calculate the total.