Thank you, this code was very useful! I was able to redo my comparison, but I am not able to get the same number of MS/MS matched between the console and GUI
There are the same number of peaks detected(2,028), but there are different MS/MS matched peaks. GUI MS/MS matched: 125 console MS/MS matched: 78 overlap between GUI and console: 56
Are there parameters only tunable from the GUI for lcmsdda related to isotopes/adducts/neutral loss that are not available in the console maybe? I attached an excel file comparing my gui parameters vs console config.
So what you what you have now is: #Project MS1 Data type Centroid MS2 Data type Centroid Ion mode Positive Target Metablomics Mode ddMSMS
#Adduct ion setting [M+H]+
This should become: #Project MS1 Data type: Centroid MS2 Data type: Centroid Ion mode: Positive Target: Metablomics Mode: ddMSMS
#Adduct ion setting Adduct list: [M+H]+,[M+NH4]+,[M+Na]+
As a note I am not able to reproduce the results I have in the GUI with the mac consoleApp (GUI produced 2x more annotations and 2x more adduct types are found in the 4.38 GUI vs 4.48 mac console with parameters exported from the GUI), so there may be more differences with row names than using colons that I am unaware of.
Anyone who could clarify this would be greatly appreciated.
