Metabolomics Society Forum

Software => MS-DIAL => Topic started by: Sebas on October 13, 2020, 09:20:22 AM

Title: Normalization
Post by: Sebas on October 13, 2020, 09:20:22 AM
Hello everyone, Hello Hiroshi,

is it possible to normalize by "ref matched" directly in the software? like TIC of ref matched metabolites ?;

For lipidomics studies, is it possible to normalize by "lipid class of ref matched" directly in the software ?


Best regards

Sebas
Title: Re: Normalization
Post by: Hiroshi Tsugawa on October 30, 2020, 11:09:25 AM
Hi Sebas,

this can be performed by selecting "mTIC" normalization method of MS-DIAL normalization option.
However, I found a bug here now... mTIC option now includes "suggested" metabolite's information as well.
Now I have fixed the issue, and I will upload the new version next week.
Thanks,

Hiroshi
Title: Re: Normalization
Post by: Hiroshi Tsugawa on November 01, 2020, 07:33:22 AM
Now, the new version is online.
http://www.metabolomics-forum.com/index.php?topic=1576.0

Thanks,

Hiroshi
Title: Re: Normalization
Post by: Sebas on November 02, 2020, 03:22:32 AM
Thank You very much Hiroshi
Title: Re: Normalization
Post by: Sebas on November 02, 2020, 04:27:33 AM
Hi Hiroshi, i try the new version of MsDial.
Thank you very much for your rapidity.

When I removed manually some "Ref Matched" metabolites in the show ion table of the alignement result, some "Ref Matched" is removed of the table. But if i apply a normalization (mTIC), save it, export the normalized data, the sum of total of Ref Matched in the Excel is not 1, certainly due to the manually 'Ref Matched" removed.

Have a good day

Séb
Title: Re: Normalization
Post by: Hiroshi Tsugawa on November 22, 2020, 07:04:20 AM
Hi,

simply, I wrote the source code to let you know how the mTIC value is calculated.
Here, LibraryID should be more than 0 if a peak is annotated by MSP library.
The postidentificationlibraryID should be more than 0 if a peak is annotated by user-defined text library containing the pair of m/z and retention time. The annotated metabolite having the tag of "w/o MS2" is excluded to calculate the mTIC value.
Thanks,

Hiroshi

Code: [Select]
for (int j = 0; j < alignedSpots.Count; j++) {
           if ((alignedSpots[j].LibraryID >= 0 && !alignedSpots[j].MetaboliteName.Contains("w/o")) || alignedSpots[j].PostIdentificationLibraryID >= 0)
                        tic += alignedSpots[j].AlignedPeakPropertyBeanCollection[i].Variable;

                    }
                }

Title: Re: Normalization
Post by: Sebas on December 08, 2020, 09:03:45 AM
Thanks Hiroshi!!
Great job!