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systemsomicslab / MsdialWorkbench

Universal workbench incorporating msdial, msfinder, and mrmprobs
https://systemsomicslab.github.io/compms/msdial/main.html
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Parameter setting of medial command line #212

Open FunkiiL opened 11 months ago

FunkiiL commented 11 months ago

Hi all,

I plan to use medial command line to do alignment since I have too many samples. But I have 2 questions.

  1. How to specify the order of the sample sequence in ms-dial command line in the parameter setting? The sequence of the output file looks randomly but I want to set the file type and class of each sample.
  2. I have added map file in parameter setting which is shown in the attached photo. But how to make sure the msp file is used and the compound ID managed in the output msdial file from command line. image

Thank you very much!

ondrej-kuda commented 7 months ago
  1. The primary order is based on time/date of the files, assuming they were acquired in a sequence. MsdialConsoleApp creates a new class for each file. You can change it later using GUI, manually in the exported files, or change the code itself and build you own version.
  2. The parsed field is msp file, e.g. 
    #Identification
#MSP file and MS/MS identification setting
msp file:/home/user/msplibs/pos/NIST20pos.msp

and eventually the text file field for RT m/z list.