I upleaded a mzML file (directly exported from Shimadzu software) into MSDIAL and noticed, that MSDIAL didn't contain all compounds from the mzML file. I tried different uploading parameters, especially for peak detection and went even down to a minimum peak height of 0. I found a similar question from April 7th 2021, which was about internal standard masses not being displayed in MSDIAL, but this problem was also not entirely fixed just by adjusting the uploading parameters. Now my question is, what all the reasons could be, for MSDIAL not displaying all the data?
The file I used can be found here: mzML-example-file
I'm very thankful for tips and help,