Text only | Text with Images

Metabolomics Society Forum

Software => MS-DIAL => Topic started by: spapaz on April 22, 2020, 08:14:35 AM

Title: Isotopes
Post by: spapaz on April 22, 2020, 08:14:35 AM
Hi Hiroshi,

it seems that isotopic patterns are recognized (visible in the Peak Spot), but are not exported in the msp and mgf files.
Is it possible to include them?

Thanks

Stefano
Title: Re: Isotopes
Post by: Hiroshi Tsugawa on April 25, 2020, 12:21:04 AM
You can export both ms1 isotopic ions and ms2 by using MAT file export function. Just right click on the peak spot viewer of main window, then formula and structure search, then add components to search list.

The direction will generate mat files for peaks that you are interested in.
Thanks,

Hiroshi
Title: Re: Isotopes
Post by: spapaz on April 28, 2020, 08:01:56 AM
Thank you Hiroshi.
And instead, from the option menu: "Export" -->Peak List result,
would that work too to include isotopes? It seems is possible to define the isotope region (default 5 Da).
The export format make any difference if the exported file will include or not the isotope patterns?
E.g. mgf, mat, txt, msp...

Thanks

Stefano
Title: Re: Isotopes
Post by: Hiroshi Tsugawa on April 30, 2020, 12:32:54 AM
Hi,

the tab-delimited text format should contain the isotope information as well!

Hiroshi
Title: Re: Isotopes
Post by: spapaz on April 30, 2020, 08:05:12 AM
Hi Hiroshi,

Thanks. It would be great to export the aligned feature IDs as mgf, containing both MS1 and MS2 levels.
This in order to import it into Sirius, which recognize isotope patterns at the MS1 level

But as I understand it is currently not possible in MS-DIAL? I know it is possible in mzMine or OpenMS.
Of course the other option is to process the raw files in Sirius, but it would be great if MS-DIAL could also interface with Sirius

Thanks!

Stefano


Title: Re: Isotopes
Post by: Hiroshi Tsugawa on May 06, 2020, 12:34:06 AM
Hi, I will support to export the results as .ms format in future to be used in sirius as well!
Thanks,

Hiroshi
Title: Re: Isotopes
Post by: Hiroshi Tsugawa on May 06, 2020, 12:36:34 AM
BTW, my current plan itself is that MS-DIAL will not implement Sirius program internally (because I can make the similar function by myself). Of course, one can implement Sirius by modifying the source code of msdial.:)
http://prime.psc.riken.jp/compms/msdial/main.html

Hiroshi

Title: Re: Isotopes
Post by: oscardr on December 03, 2020, 01:38:30 AM
Hi,

Hiroshi thanks for your work. do you have any update regarding exporting as .ms so we can have both ms1 and ms2 ready for SIRIUS?

thanks !
Title: Re: Isotopes
Post by: Hiroshi Tsugawa on December 25, 2020, 09:45:14 AM
Hi,

sorry, at this moment, I do not have much time to work for this because we are now making new msdial structure for further updates (completely by different source codes). In future version, this function will be included.

Thanks,

Hiroshi
Text only | Text with Images