You can use the labile mode in FragPipe, described here:

https://fragpipe.nesvilab.org/docs/tutorial_labile.html

Thank you very much for your reply. But I still have some questions for you. In order to see the isocyanate dissociation that is often seen with citrulline. I used the following parameters to set up the detection of the HNOC diagnostic ion peak and the H11C5N3O citrulline dissociation residue (129.09 Da).I am not sure if this is the correct setting?

Other than that, I don't seem to see the delta mass column in my psm.tsv file with any information related to the diagnostic ion peaks, etc. that I've set up. Is it possible that I've set it up incorrectly?Very much looking forward to your reply and thank you for your selfless help!

Best,
liangxiao

You can use the labile mode in FragPipe, described here:

https://fragpipe.nesvilab.org/docs/tutorial_labile.html

Hi liangxiao,

It looks like you need a couple of changes to the parameters. The m/z of the immonium ion should be specified as a diagnostic ion, and needs to include the mass of the charging proton since it needs to be m/z rather than mass (so 130.0975 not 129.09). The fragment remainder ion is calculated starting from the mass offset, so for isocyanate loss, it would be 0.984 - 43.01 = -42.026 (it's negative because the loss is larger than the original modification mass). You also need to turn on "Localize mass shift (LOS)."

I would also suggest that you specify deamidation as a variable modification (0.984 on NQ) and then restrict the mass offset 0.984 just to R, as that will link the diagnostic and remainder ions only to citrullination and not deamidation.

Finally, you will see the modifications in the Assigned Modifications column in the psm.tsv table, not the Delta Mass column, because you have opted to remove delta masses ("Yes, remove delta mass").

Best,
Dan

Hi liangxiao,

It looks like you need a couple of changes to the parameters. The m/z of the immonium ion should be specified as a diagnostic ion, and needs to include the mass of the charging proton since it needs to be m/z rather than mass (so 130.0975 not 129.09). The fragment remainder ion is calculated starting from the mass offset, so for isocyanate loss, it would be 0.984 - 43.01 = -42.026 (it's negative because the loss is larger than the original modification mass). You also need to turn on "Localize mass shift (LOS)."

I would also suggest that you specify deamidation as a variable modification (0.984 on NQ) and then restrict the mass offset 0.984 just to R, as that will link the diagnostic and remainder ions only to citrullination and not deamidation.

Finally, you will see the modifications in the Assigned Modifications column in the psm.tsv table, not the Delta Mass column, because you have opted to remove delta masses ("Yes, remove delta mass").

Best, Dan

Thank you very much, I reset the parameters as you suggested and the results appeared.

Best,
liangxiao

After search, how to check which peptide including the diagnostic ion in output files?

@douyue623 I think you have posted a new issue here #1651 . Please do not abuse the GitHub issue.

Best,

Fengchao