DIA-NN: Propagate Information finished, exit code: 1

[alexziegler8]

Hi,

I've had a similar issue to #1815 in where I have included peptide C-terminal modifications to my search and it resulted in this exit code in DIA-NN. I am fairly sure PTM prophet is disabled (the box is not ticked). All other DIA-NN outputs previously generated were all correct - does this step add any additional information or could I use what was previously generated (report.pg_matrix/report.pr_matrix)?

Thank-you,
Alex.

log_2025-01-31_18-48-43.txt

[fcyu]

Hi Alex,

Thanks for the feedback. I don't the C-term modification is well supported because DIA-NN doesn't have a "marker" or "placeholder" for the C terminal.

Taking RMPC(UniMod:4)AEDYLSVVLNQLC(UniMod:4)VLHEK(UniMod:734) and AAVEGTVEAGATVESTAC(UniMod:4)(UniMod:734) for example, the first peptide is a bit misleading because the (UniMod:734) is not on K but on C-term. I am not sure if there is an easy unless we take the MSFragger modification settings when parsing DIA-NN's output.

Best,

Fengchao

[alexziegler8]

Hi Fengchao,

Yeah that makes sense! Thank-you for the clarification,

Alex.