Thoughts based on ProForma spec discussion

[douweschulte]

Based on the discussion of ProForma 2.1 in the HUPO-PSI spring meeting.

• Modify parser to be verifying ProForma 2.0/2.1 (parameter to turn this on, then generate warnings)
• Finish implementing 2.1
• Handle INFO mods better
• Handle the Unimod XML instead of OBO
• Build function to check for equality between peptides, how similar are they (same mass, same mods, equivalent mods (eg defined as identical in the cross-ids))
• Normalisation of ProForma strings (as part of online verifying tool) (also translation to simpler format, eg get equivalent mods from simpler ontologies or replace with the correct formula)
• Export parsed peptide as generic schema?
• Could cross-linkers have neutral losses?