Table 1.
Comparison of the Supported Features of ProForma 1.0 and 2.0
| feature | ProForma 1.0 | ProForma 2.0 |
|---|---|---|
| protein modifications designated by CV/ontology names and accession numbers | ✓ | ✓ |
| representation of glycan composition | ✓ | ✓ |
| N-terminal and C-terminal modifications | ✓ | ✓ |
| delta mass notation for modifications | ✓ | ✓ |
| information tag | ✓ | ✓ |
| joint representation of experimental data and interpretation | ✓ | ✓ |
| NEW support for elemental formulas | limited | ✓ |
| NEW representation of isotopes | limited | ✓ |
| NEW cross-link notation | X | ✓ |
| NEW representation of interchain cross-links | X | ✓ |
| NEW representation of disulfide linkages | X | ✓ |
| NEW representation of glycans with GNO ontology as CV | X | ✓ |
| NEW specifying a gap of known mass | X | ✓ |
| NEW labile modifications | X | ✓ |
| NEW unknown modification position | X | ✓ |
| NEW possible set of modification positions | X | ✓ |
| NEW representation of ranges of positions for the modifications | X | ✓ |
| NEW modification position preference and localization scores | X | ✓ |
| NEW scoring for ranges of positions for a modification | X | ✓ |
| NEW fixed protein modifications | X | ✓ |
| NEW ambiguity in the order of amino acid sequences | X | ✓ |
| NEW representation of ion charges and more than one peptidoform per spectrum | X | ✓ |
| NEW representation of branched peptides | X | ✓ |
| NEW representation of ambiguity in the order of the amino acid sequence | X | ✓ |