Peptides with and without modficiation

[tanjagosnjak]

Hi,

I am performing searches with different modifications. In my searches, whenever there's a modification present, only the modified peptide is reported, and the exact same peptide without modifications is never found. I am comparing results with other softwares and they sometimes find the same peptides with and without modifications. Is there a setting that I might be missing that could produce reports showing both modified and unmodified peptides?

Thank you, Tanja

[danielgeiszler]

Please post your log.

Best, Danny

[tanjagosnjak]

log_2024-03-29_21-18-52.txt

[danielgeiszler]

You're doing an open search. The only modifications you're searching for directly are variable oxidation of M and fixed alkylation of C.

Can you please upload an example of the issue you're having?

[tanjagosnjak]

Yes, that's right.

For example, MS Fragger reports about this peptide with modification

but MaxQuant reports about the same peptide with and without modification

I understant that results can't be the same, but I can't find an example where MSFragger has found beside the peptide with modification also one without it.

So I would like to know if there is a possibility to enable the software to also report an unmodified sequence if there is one.

[danielgeiszler]

Are you looking at the combined_peptide.tsv table or the combined_modified_peptide.tsv table?

The combined_peptide.tsv collapses all modification states into a single row. If you want to see different modification states, you need to look at the combined_modified_peptide table.

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

[tanjagosnjak]

I am looking at peptide.tsv files. I can't find those files with prefix 'combined'.

[anesvi]

You should be looking at PSM.tsv file

[tanjagosnjak]

thank you for your help