I am using two spectral libraries to annotate HPLC-MS DDA data, with the default MSDIAL parameters, and I see that the two resulting feature tables have a different number of features despite using the same spectral dataset as input.
The sample types (samples, QCs and blanks) were provided, and the option "Remove features based on blank information" was not checked.
Is there any way to avoid MSDIAL to filter features out? I would like to keep the same number of features to compare the annotations obtained with the 2 libraries.