Previous versions of MS Amanda (v2.0.0.20554 and below) provided only limited possibilities for automatic rescoring of output files. While the Proteome Discoverer (Thermo Fisher Scientific) variant of MS Amanda facilitated its integration with Percolator, the standalone version did not accommodate a user-friendly interface to link with downstream rescoring techniques. In addition, the CSV output files only contained a limited number of columns that could be utilized as features for rescoring, i.e., Amanda score, weighted probability, precursor mass-to-charge ratio, precursor charge, retention time and the number of matched peaks.