When you work with several datasets in one go, it can often be useful to know HOW close the individual datasets are to each
other, WHAT precursors are present across the files and WHERE the differences are between the runs.
The compare files window displays the precursors in two datafiles at a time, along with what precursors they have in common,
and what are unique to each file.
The columns on the right display the mass of each precursor, along with information whether it is in file A,B or in both.
You can then save the scans referring to these precursor values into new, individual mgf files.