Is there a way to export ONLY the MSMS peaks as a msp or mat to bring into MSFINDER? For instance, when looking at MSMS data files, MSDIAL will align non-MSMS peaks and it seems like if I Export > Peak list (as mat or msp), it will export all peaks, not just the MSMS ones?
I'm trying to screen some GC-QTOF data through a MSP library and for some features that are perfectly aligned, it chooses the sample with the lowest intensity to do the library matching with. For example (screenshots), the 10ppb std has an intensity of 1822 where the other standards are >20,000, yet it tried to do the library match with the 10ppb std and failed to ID the correct compound (decachlorobiphenyl).
How does it choose which sample it uses to do the library matching? Is there a way to override it? Or is there a setting where we can tell it to use whichever sample has the highest intensity?
