As more platforms are developed to identify proteoforms, a central ambiguity has arisen – precisely what is meant by a ‘proteoform identification’. Small variations in the definition of an identification can make comparing results across laboratories very difficult. To address this a multi-level system is proposed that accommodates the four classes of ambiguity:

  • PTM localization: a PTM is not localized to a specific amino acid.
  • PTM identification: there is ambiguity in the identity of a PTM.
  • Amino acid sequence: there is ambiguity in the amino acid sequence.
  • Gene: the gene of origin is unknown or ambiguous.

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