Hello,
In MS-Dial it should be possible to merge aligned LC-MS feature lists from pos and neg data recorded for the same samples and I have tried using the amalgamation function but I cannot get it to work - either nothing happens or MS-Dial crashes. Can anyone perhaps give me an example on what the .txt feature list that should be created for one polarity should look like? Or perhaps let me know how to do this :)
Thanks!
Anna
Hi Anna,
I would like to suggest you trying MSCleanR (A shiny R package).
Best,
Sukis
Dear Anna,
I was recently asked for the same question by a user. But I cannot reproduce the crash issue.
First, the attached file extracted from negative ion mode data is the list to be used in positive ion mode.
Then, if it works, you can see the result e.g. in MS-DIAL GUI by changing "Label" of top-left panel (peak spot navigator) to "Adduct" as attached. And the result is also described in the exported data matrix.
Please let me know your update.
And yes, MS-CleanR should be one option to clean-up your data.
Thanks,
Hiroshi
Dear Anna and Hiroshi,
I know this topic is very old, but I was having the same issues as Anna but I solved the issue (at least mine).
In Section 5-12-2 of the MSDIAL tutorial (https://mtbinfo-team.github.io/mtbinfo.github.io/MS-DIAL/tutorial.html#section-5-12-2), Step #1 says to export "Peak list result", and later on in the image below Step #4, the peak list (from a sample, instead of the alignment result export) is being applied to the Alignment Spots. I did not have a crash when the alignment export from positive polarity is applied to the alignment spots in negative polarity, and vice versa.
Another source of this crash can be the advanced settings under the MS2Dec tab of the MSDIAL project processing parameters. When isotopic peaks are not filtered, this also causes a crash.
I hope this post helps others with a similar issue in the future.
Cheers,
Triston