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Metabolomics Society Forum

Software => MS-DIAL => Topic started by: QizhiSu on October 30, 2020, 08:20:35 AM

Title: MS-DIAL does not export MRMPROBES library correctly
Post by: QizhiSu on October 30, 2020, 08:20:35 AM
Hi,
I have a problem with exporting MRMPROBES library. I have manually curated my UPLC-QTOF-MS data and used the default parameters to export MRMPROBES library. However, the exported table looks weird and is not the same as my identified table (see attachments).

Does anybody have experience?

best,
Sukis
Title: Re: MS-DIAL does not export MRMPROBES library correctly
Post by: Ondrej on October 30, 2020, 04:21:59 PM
Hi,
what is the problem? It looks fine. You can probably play with deconvolution params in MS-DIAL to get cleaner spectra and more reasonable MRMs.
Ondrej
Title: Re: MS-DIAL does not export MRMPROBES library correctly
Post by: Hiroshi Tsugawa on October 30, 2020, 08:13:37 PM
Maybe...Please untick "use reference spectrum" in MRMPROBS library export settting.
Thanks,

Hiroshi
Title: Re: MS-DIAL does not export MRMPROBES library correctly
Post by: QizhiSu on October 31, 2020, 02:21:36 AM
Hi Ondrej,
The problem was that the exported file is different from my table list.

best,
Sukis
Title: Re: MS-DIAL does not export MRMPROBES library correctly
Post by: QizhiSu on October 31, 2020, 02:26:15 AM
Hi Hiroshi,
I have tried to untick "use reference spectrum", but the result is even worse.
Title: Re: MS-DIAL does not export MRMPROBES library correctly
Post by: Hiroshi Tsugawa on November 01, 2020, 07:32:05 AM
Hi Sukis,

I found the bug, and fixed it. Today, I released the new version of msdial program. Here, you can export the reference library correctly.
http://www.metabolomics-forum.com/index.php?topic=1576.0
Thanks,

Hiroshi
Title: Re: MS-DIAL does not export MRMPROBES library correctly
Post by: QizhiSu on November 02, 2020, 07:48:43 AM
Hi Hiroshi,
I have tested the latest version. It works fine now. But it still includes compounds that have already been denied as identified during manual curation.  Anyway, it is fine. I can manually delete them.

Thanks a lot.
Sukis
Title: Re: MS-DIAL does not export MRMPROBES library correctly
Post by: QizhiSu on November 02, 2020, 03:56:46 PM
Hi Hiroshi,
Just one more thing. I found the latest version MSDIAL exports all initial identification by the software itself but ignores all manual curation even though I have ticked the ref.match box.

Best,
Sukis
Title: Re: MS-DIAL does not export MRMPROBES library correctly
Post by: Hiroshi Tsugawa on November 22, 2020, 07:27:29 AM
Hi Sukis,

for this issue, I cannot reproduce your issue.
For example, how do you exclude automatically annotated metabolite information in MS-DIAL?
I personally tried to do it with Control+D that converts the annotated information (library ID >= 0) into unknown (library ID < 0).
As long as I use this, the exported reference library with the option of "Use reference spectrum to make MRMPROBS library". If you untick this option, the program always exports all peaks.

Thanks,

Hiroshi
 
Title: Re: MS-DIAL does not export MRMPROBES library correctly
Post by: QizhiSu on November 22, 2020, 08:24:52 AM
Dear Hiroshi,
You are true. The problem was that I didn't untick "Use reference spectrum to make MRMPROBS library". It works perfectly now.

Best,
Sukis
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