For exemple, if you've added a new modification in Mascot with same composition/mass than an other one (to group modifications for instance):

• Mascot Modification: Propionyl on S / T  with different 'group'.
• Add Modification: Propionyl_ST on S / T in same group.

In Proline, after importing and running some process on a dataset corresponding to a Mascot search (B.dat) using Propionyl_ST, the modification associated with a peptide is "Propionyl (S1)" and not "Propionyl_ST (S1)"

--- 

Here is the explanation why this occurs. This problem is not fixed yet.

When you import a file A.dat with  Propionyl (S) and Propionyl (T) as variable PTMs and peptides with one of this modification, Proline

• creates a PTM object “Propionyl (S)” (idem for (T) ...)
• creates a peptide with a link to that PTM and with a “readable_PTM” property = “Propionyl (S1)”

When you import your new file B.dat, with  Propionyl_ST (ST) as variable PTM, and peptides with this modification : 

• before creating the PTM objects, Proline will verify that these PTMs do not already exist in your project. In this case,  Propionyl_ST in B.dat is the same PTM as  Propionyl in A.dat (same delta mass, same composition H(4) C(3)).
  So there is no new PTM created.
• during the import, the “readable_ptm” of the peptide is created from information read in the B.dat file. The readable_ptm = “Propionyl_ST (S1)” in the dataset from B.dat. So you don’t see that the PTM associated to this peptides is “Propionyl (S)” and not “Propionyl_ST (S)”. This is not a problem, PTMs are identical  !

Now, when you create a new dataset from the dataset “B.dat”, by merging it or using it for a quantitation.  The peptide’s “readable_ptm” property in this new dataset is created from the PTMs associated to the peptide. Here, it will use "Propionyl (S)" so the “readable_ptm” property of the peptide will be “Propionyl (S1)”.