All modified peptides have zero intensity when quantifying with labile-phospho.

[POde97]

Hi all,

I can't understanding why all the peptides are quantified to zero intensity when using labile-phosphor default workflow despite the flag ionquant.run-ionquant=true in the workflow file. (While when using LFQ-phospho I get a proper quantification )

Also is not totally clear to me the structure of the output and why I'm not getting anymore the combined_modified_peptide.tsv If I well understood some of the informations that can be found in the combined_modified_peptide.tsv are present in the msstats.csv but still every PTMs has zero intensity. Further it is not super clear to me what is the combined_protein.tsv output of labile phospho. Also following the tutorial https://fragpipe.nesvilab.org/docs/tutorial_labile.html I noticed that I'm not getting any psm.tsv from the labile-phosphor workflow.

Can you please help me in understanding what I'm doing wrong? I attached my log

Thank you in advance !

log_2024-10-17_14-53-06.txt.zip

[fcyu]

You should also set quantitation.run-label-free-quant=true as well.

Best,

Fengchao