MassAI assigns a score to every protein that has been identified in a dataset. The value is a figure of how well the protein is
represented in the dataset, based on the number of observations, quality of same and peptide coverage. Sometimes however, we
may be interested in hand-picking certain proteins while ignoring others - although these might be high-scoring ones.
MassAI has a feature for manually validating, retaining or discarding proteins. These are then transferred into the "Manually Validated
Proteins" window, or MVP. In the example below, we see the standard scan-by-scan result list following a search against the murine
proteome. Apolipoprotein is represented in a number of high scoring scans, and we wish to keep it for later use.
Normally we LEFT-click on any row in the result window, which then brings up the annotated scan.
In this case however, we RIGHT-click instead. This brings up a menu, from where we can choose to "add the protein to the manually
This opens the MVP window automatically, and adds the protein to the list.
Furthermore, all scan results relating to that same protein are coloured green.
Instead of adding the selected protein to the list, you can opt to discard the protein, in which case every result from this protein is
coloured RED, or label it as "maybe" if in doubt. This colours all results YELLOW.
Once you are happy with your list of manually validated proteins, use the FILE menu in the MVP window to export the sequences into
a new FASTA file.