From our Consortium Paper in Proteomics.
"The issue of proteoform and PTM scoring arose during workshops and consortium meetings and was identified as a key ambiguity in the field that needs to be addressed."
"An initial tool was developed for scoring proteoforms of multiply-modified proteins. The input is: (i) an intact mass, (ii) a fragment ion dataset, (iii) a protein sequence, and (iv) the specific kinds of PTMs to be considered. The output is given as a [Phrap] score, where the higher scores are better. Initial use of the tool (available on the website of the Consortium for Top Down Proteomics) is in progress. This software is ongoing in its development and represents our initial attempt to address the pressing issue of formalizing confidence in proteoform characterization."