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h4. Fixed Modifications
For this converter, a "fixed" modification is defined as any one that occurs universally for all amino acids of a certain type, but which is NOT written into the peptide sequence in your TSV file - it's simply assumed for all occurrences of that amino acid.
| *If the mass offset does NOT appear in the peptide string, but is simply assumed for all amino acids of a certain type, then it should go under "Fixed Modifications".* |
When entering references for fixed modifications, use the same procedure as for variable modifications [above|#Variable_Mods], except keep in mind that it's only "fixed" if the mass shift is missing from the peptide string. Therefore, the pattern entered in the small text box should consist only of the relevant amino acids, since that's all that will be found in the peptide string to reflect this modification: