Missing 'Assigned Modifications' for N-terminal mods in detailed mass-offset search

[tjlundgren]

Hello Fragpipe team,

I am trying to analyze results from a mass-offset search. In the psm.tsv output, there are some PSMs with a reported 'Modified Peptide' but no 'Assigned Modification'. These only occur when the modified aa is at the N-terminus of the peptide, but not all N-terminal modifications are missing the 'Assigned Modification'.

Is there a reason some modified peptides are not given an 'Assigned Modification' output?

Note the option to 'report mass shift as a variable mod' is set 'Yes, remove delta mass' to make IonQuant happy, but I am trying to calculate the precise total delta mass (including shift) for filtering the data. I have done this with the 'Assigned Modification' output, but the integer value in 'Modified Peptide' alone may not be sufficient.

Fragger params and example psm.tsv: https://drive.google.com/file/d/1cGJI8GxfUTs30An2zvGZdfJPxZroWtD8/view?usp=drive_link