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Messages - Ipputa Tada

1
MS-DIAL / Re: MS-DIAL crash when openning corrDec spectra
Dear Sukis,

Thank you very much for the bug report. I am sorry for my late reply.
I am the main developer of CorrDec. I fixed the bug and the new MS-DIAL version will be released soon.

MS2Dec and CorrDec are different algorithms based on different concepts. They are pros and cons, so please use them separately.
Changing the selected spot will also update the CorrDec window, so you can check it as same as MS2Dec.

Best regards,
Ipputa
2
MS-DIAL / Re: Exporting CorrDec spectra
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
3
MS-DIAL / Re: Exporting CorrDec spectra
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
4
MS-DIAL / Re: Correct settings for GNPS/FBMN from MSe data
Dear Taylan,

I am the main developer of Correlation-based Deconvolution (CorrDec).
CorrDec is an MS2 deconvolution method using the intensity correlations between MS1 and MS2 among samples to obtain clean MS2 spectra.
User can run CorrDec after data processing, please see the following topic:
http://www.metabolomics-forum.com/index.php?topic=1406.msg4146#msg4146

MS-DIAL can show CorrDec spectra and export them to MS-FINDER or as MSP format.
However, currently, CorrDec cannot deconvolute MS1 features, and CorrDec spectra cannot be exported to GNPS.
If you are interested in CorrDec, please try with default parameters.

Best,
Ipputa
5
MS-DIAL / Re: internal Standard
Hi,

I am the main developer of "correlation-based deconvolution" (CorrDec).
CorrDec requires more than 6 samples (>30 is better) to calculate correlation among samples.

- Setting and run
This is the main function, CorrDec will run for all alignment spots.

- Identification
The identification process will start using the CorrDec spectra.

- Run single spot
This is a quick function as a test. CorrDec will run for a selected alignment spot.

- Show CorrDec spectra
CorrDec spectra window will be launched to check the results.

Best,
Ipputa