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muda.pl is an evaluation script (written in Perl) without great dependencies.
It congregates information from 4 different MaxQuant output files into a master file suitable explicitly for protein neo-termini analyses. The central anchor for the data congregation is the modificationSpecificPeptides.txt file - additional data is inferred from different other source files from the MaxQuant txt folder but the starting point for the data assembly is solely the modificationSpecificPeptides.txt file. ...