Advice for validating non-target analysis with known compounds

[akogler]

Hi, this is more of a general question than an issue. I am using patRoon for non-target analysis but I spiked some known compounds into all of my samples to validate the non-target analysis. During formula annotation, the formulas corresponding to the known compounds show up as candidate formulas. However, during compound annotation, only one of the known compounds shows up. I have tried to adjust some parameters for compound annotation and MS peak list generation, but none of the changes have improved the output. Do you have additional suggestions for troubleshooting? Thank you!

Here is an example of my compound annotation command: compounds <- generateCompounds(fGroupsSelSusp, mslists, "metfrag", method = "CL", dbRelMzDev = 5, fragRelMzDev = 5, fragAbsMzDev = 0.002, database = "pubchem", topMost = 2500, timeoutRetries = 5, errorRetries = 5, maxCandidatesToStop = 2500)

I have varied dbRelMzDev, fragRelMzDev, and fragAbsMzDev and have also tried different combinations of the scoring types allowed for Metfrag initially with equal weights but then also with different weights.

For MS peak list generation, I use the following command: mslists <- generateMSPeakLists(fGroupsSelSusp, algorithm = "mzr", maxMSRtWindow = 5, precursorMzWindow = NULL, topMost = NULL, avgFeatParams = avgMSListParams, avgFGroupParams = avgMSListParams)

I have adjusted clusterMzWindow, topMost, pruneMissingPrecursorMS, minIntensityPre, and minIntensityPost when setting avgMSListParams.

Thanks for any pointers!