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Topic: Exporting CorrDec spectra (Read 351 times) previous topic - next topic

Exporting CorrDec spectra

Dear Dr. Tada and Dr. Tsugawa,

How can I export CorrDec results as an MSP file? I searched the MS-DIAL tutorial, this forum, and Google, but I did not find any information about this.

If I should export using the "Export -> Alignment results" option, how do I know whether I am exporting the CorrDec spectra or the MS2Dec spectra?

Can I download all of the CorrDec spectra from the alignment results at once, or do I need to download them one by one?

Related posts:
http://www.metabolomics-forum.com/index.php?topic=1410.msg4165#msg4165
http://www.metabolomics-forum.com/index.php?topic=1406.msg4146#msg4146

Thank you for your help.

Kind regards,
Taylan

Re: Exporting CorrDec spectra

Reply #1
Dear Taylan

Thank you for creating this topic.
Users cannot change the deconvolution method for exporting in current MS-DIAL (MS2Dec is the default), sorry for the inconvenience.

Bulk export methods were already developed, but not officially released yet.
We will release a new MS-DIAL version with bulk export functions in early June 2020.


Tips to export all CorrDec spectra as an MSP file using current MS-DIAL.
Users can export all CorrDec spectra to MS-FINDER in a project launched as "Multiple CEs mode (MS method type)", then MS-FINDER can export all records as a single MSP file.
1) Launch "Alignment Table" by clicking "Show ion table" on MS-DIAL main window
2) Click bulk export to MS-FINDER button on "AIF Viewer Controller" (Alignment Table Viewer will be changed to MS-FINDER exporter form)
3) Click "Export" button on the exporter and choose an export folder (MS-FINDER will be launched).
4) In the MS-FINDER, click "Export" (menu bar) -> "Export peak annotation result as MSP format"
Only in this way, all CorrDec spectra can be exported at once even in MS-DIAL v 4.20 or earlier.

Best regards,
Ipputa

Re: Exporting CorrDec spectra

Reply #2
Dear Dr. Tada,

Thank you for those detailed instructions.

I was able to do a batch export to MS using MS-DIAL v4.20 and MSFINDER v3.40. However, the MS method type of my project is "SWATH-MS or conventional All-ions method" (MSe), not "All-ions with multiple CEs..." as you instructed. It still worked, though...

How do I know if the exported spectra are CorrDec, MS2Dec, or not deconvoluted? I did not see any indication of this on any of the screens.

Also, the steps I followed were slightly different that what you described:
1) [same]
2) The button that I clicked (see top left corner of attached picture) says "Export to MS-FINDER" when I hover over it.
3) [same]
4) [same]

Thank you,
Taylan

 

Re: Exporting CorrDec spectra

Reply #3
Dear Taylan

Sorry for my late reply.

MS-DIAL v.4.20 cannot export all CorrDec spectra at once in "SWATH-MS or conventional All-ions method" project. Sorry for the inconvenience, we will fix this issue in the next version.

By your steps, MS2Dec spectra will be exported. We will also make a function to select the target spectra type (MS2Dec, CorrDec, or raw).
 
Best regards,
Ipputa