The Tool Buttons - MGF filter
The MGF filter contains various algorithms for cleaning up your dataset prior to a search.

When you use MGF filter to work on your datasets, MassAI creates a new set of MGF files, while no changes are made to your original
files. You can work with a single file at a time, or do a whole batch of files in one go.
In the limiter, you can set the maximum number of peaks that you wish to retain in each scan (default is 125). The filter keeps
this number of the most intense peaks, while low intense peaks are filtered away.

You can also set limits for the minimum number of peaks to a scan, so that you do not export scans devoid of peaks, set a
cutoff for the precursor intensity, to cut down on the number of scans where there simply is not engough material to fragment
and so on.
The noise filter makes a fingerprint of the ion abundance throughout your dataset. If you have a tryptic digest of a dataset, we
expect the y1 (LYS or ARG) ions to be dominant. Other peaks that are more abundant than this are most likely some type of
noise, or non-peptide contaminants.

In the example below, we observe a pattern of peaks that are more abundant than the Y1(K), Y1(R) and Y2 ions.
By putting these peaks into an exclusion list, we can remove non-relevant signals from our dataset prior to searching.
Below, the EXCLUSION list has been populated with the values from the noise filter.
You can use the INCLUSION list to enrich your dataset for scans containing specific peaks of interest. This could be the
obvious Y1 and Y2 ions from a tryptic digest, known reporter ions or oxonoum ions from glycosylations.

You can edit your own inclusion/exclusion list by pressing the "E" button and import them by pressing the "L" button.