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Metabolomics Society Forum

Software => MS-DIAL => Topic started by: QizhiSu on January 15, 2020, 11:53:43 AM

Title: How MS-DIAL calculates the "fill"
Post by: QizhiSu on January 15, 2020, 11:53:43 AM
Hello, Hiroshi,

Could you please explain to me how MS-DIAL calculates the "fill"? because I found that in many cases, the S/N ratio of a certain alignment spot in many samples is small than that in blanks, but not 0.  Will those samples be included in the "fill"? I am guessing that MS-DIAL calculates S/N or height/area of each spot once it detects the quan mass. but it seems more reasonable to calculate those values only when the spectrum correspondent to that spot, let's say when spectrum similarity higher than 80%. by this way, we can know which samples really contain that component. because when i checked my data, i found that some samples have very high S/N ratio of a certain spot, but actually the component is absent in those samples.

In addition, it will be of great help to have a single column tell that which samples have that component.

best regards,
Sukis
Title: Re: How MS-DIAL calculates the "fill"
Post by: Hiroshi Tsugawa on January 19, 2020, 09:21:56 AM
Hi Sukis,

as you can read it here (http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL/index3.html),
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.

Hiroshi
Title: Re: How MS-DIAL calculates the "fill"
Post by: QizhiSu on January 20, 2020, 01:18:13 AM
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,
Sukis
Title: Re: How MS-DIAL calculates the "fill"
Post by: Xinsong Du on March 25, 2021, 07:36:38 PM
Quote from: Hiroshi Tsugawa – on
Hi Sukis,

as you can read it here (http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL/index3.html),
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.

Hiroshi

Hi Hiroshi:

I was wondering how the S/N was calculated. It seems not related to blank subtraction. Thank you!

Best,
Xinsong
Title: Re: How MS-DIAL calculates the "fill"
Post by: Hiroshi Tsugawa on March 29, 2021, 11:57:08 PM
See from page 7 of the following pdf.
http://prime.psc.riken.jp/compms/msdial/download/mathematics/MS-DIAL%20FAQ-vs2.pdf

Hiroshi
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