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Topic: Command-line questions (Read 99 times) previous topic - next topic

Command-line questions

Hi Hiroshi and team,

I'm running MSDIAL  (v4.12) terminal version in a script as part of my automated workflow. I was getting stuck and have a few questions that hopefully you could help with. Thanks a lot in advance!

1. I can't get the compound identification working from MSDIAL terminal version.

In the method file, I have specified the path to an MSP file, however I don't see any compound annotations at all in the resulting .msdial file. I assumed that compound annotations would be indicated in the 'Title' and 'Dot product' columns of the .msdial file, is that correct?

I've attached a zip file containing method file, the msp file and the output msdial file. The same files when used with the GUI worked fine. Any chance you could take a look, that would be great.

2. Would it be possible to run the CorrDec method from the terminal? I don't see any option to specify that in the method file.

3. Can I export a peak list as .msp format from MSDIAL terminal version, instead of getting the .msdial output? This would be similar to doing to Export > Peak list result from the GUI. That would give a quick way to see the identified compounds and their spectra.

Have a nice day, and thank you so much for your help.

Re: Command-line questions

Reply #1
Hi MSDIAL team and all,

It seems that point 1 above has been fixed in the latest version (v.4.24). If somebody could help with 2 and 3 above, that would be great. Thanks.