Output

[dh2305]

Dear all,

thank you for providing a TIMS-specific rescoring platform.
I tried this tool on a MaxQuant Phospho dataset, and I was wondering what one is best supposed to do with the output.

I can assess I have increased PSM discovery but as there are no intensity attributes in the peptide output of mokapot I cannot directly continue from here.

How can I actually use the main output (psms.tsv) to make use of the increased PSM identification in the set FDR?

I was so far unable to re-import this into MaxQuant (or Fragpipe) for partial processing. I would appreciate hints at how to end up at tables akin to the original maxquant output regarding modified peptides or Phospho(ST) sites.

Best,
Dominik

[RalfG]

Hi Dominik,

Thanks for reaching out!

How can I actually use the main output (psms.tsv) to make use of the increased PSM identification in the set FDR?

That would depend on what you would like to achieve downstream. Are you interested in identified phosphosites, or in quantification info? For the former, you could filter the output on all PSMs that have a phosphorylation and pass the FDR threshold. The latter would require a bit more work, as the identifications would need to be either requantified with a tool such as FlashLFQ, or the PSM scores from MaxQuant need to be updated in the entire MaxQuant output.

We'd be happy to help you get started in any case.

Best,
Ralf