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MS-DIAL / About the use of MS-DIAL
Last post by liyong189108 -
Hi guys,
I have some questions about the use of MS-DIAL. The first question is I can not find a place to assign the internal standard when I run the latest version 4.12. The instruction say it do has a place to assign the IS. But the Instruction was written based on the version 2.28. Since the MS-DIAL has more than fifty versions, does it have a instruction about the difference of these versions?
The second question is about the result of identification.  Is the software has an access to modify the identification result?
The third question is about the result of alignment. We want to use the MS-DIAL for pathway mapping and correlation analysis of data from different platforms. But we do not know how to merge the alignment results from different platforms and use it for MS-DIAL based pathway mapping and correlation analysis.
Could you please help me?
MS-DIAL / Re: How MS-DIAL calculates the "fill"
Last post by Sukis -
Hi Hiroshi,
I understand what you mean, but it is tricky to check which samples really contain a certain metabolite manually no? I am just thinking if it is possible to include this information in the export files? that would be great.

Thank you very much.

kind regards,
MS-DIAL / Re: MSMS match main page feature does not show up in compound search list
Last post by Hiroshi Tsugawa -

yes, it's true. Sorry, probably, all users will be able to know what ms-dial does in the program for lipid annotations once I can reach to the publication of MS-DIAL 4 paper. All algorithms are there actually. I hope, it will be published in this summer...

Simply: the current MS-DIAL program performs a "hybrid" annotation system including
(1) a classical similarity matching (dot-product and reverse dot product) algorithm
(2) a rule-based decision tree algorithm to describe an appropriate structure representation of lipids by considering the mass fragment ions.

Now, the MSP file records are actually used for the first purpose (dot-product and reverse-dot product). And the spectrum similarity score is used to filter out the noisy spectra. Currently, in lipidomics project, if the dot product score is less than 0.1 AND the reverse dot product score is less than 0.5, the spectrum is recognized as "Unknown" at this stage.
Then, the mass fragment ions are evaluated by the decision tree program. In the ether PE case, the experimental spectrum is evaluated to judge if it's from plasmanyl type- or plasmenyl type. Then, if the spectrum was estimated as "plasmenyl (plasmalogen) type", the representation is changed from PE O-XX:X_YY:Y to PE P-XX:X-1_YY:Y.

Does it make sense for you?

MS-DIAL / Re: How MS-DIAL calculates the "fill"
Last post by Hiroshi Tsugawa -
Hi Sukis,

as you can read it here (,
the fill % means the "gap-filled" sample % (but 1 means 100% in the output). If you analyzed 10 samples, and if a metabolite is detected in eight samples of them, the fill % value becomes 0.8.

However, the S/N value is re-calculated in the gap-filling process. If you wanna check "which samples really contain that component", I recommend like this:

(after opened an alignment result in MS-DIAL)
1. Go to "EIC of aligned spot" tab (top panel of MS-DIAL).
2. Right click, and click "Table viewer for curating each chromatogram"
3. Here, you can check which sample has the component in the "Annotation" column.

Does it make sense for you?
Please let me know if it's helpful for you or not.

MS-DIAL / Re: How does MS-DIAL take representative spectra?
Last post by Hiroshi Tsugawa -
It makes sense for me. Of course, using the option of "identification after alignment" is good when you have many samples and many reference records.... However, I recommend to do the identification process for all samples. I think, the result of peak alignment becomes better by this because the representative spectrum can be retrieved from a spot having a good match with the reference spectrum.

MS-DIAL / internal Standard
Last post by Angrist -
Dear developers,
I would like to better understand how and where to set the information of the internal calibrants to make the normalization of chromatographic runs.
I would also like to understand what they are and how to use the parameters that show ion table and specifically Fill and Correlation
Thanks for your work, you have created a software which is the MaxQuant of Metabolomics! 8)
all the best