Re: [spctools-discuss] PTMProphet config issue

[David Shteynberg]

Hello,

Thanks for using TPP and PTMProphet.  There seems to be an issue / bug with processing c-terminal mods in this dataset.  If you are able to share this dataset for me to download I can troubleshoot the problem.

Cheers!

David

On Thu, Sep 9, 2021, 2:36 AM Mehdi Cherkaoui <mehdiche...@gmail.com> wrote:

Hi everyone, 

I use TPP (v6.0.0) to localize and score specific modifications in some datasets coming from heat induced modified proteins. I start my workflow by an X!Tandem database search, followed by a PeptipeProphet/xinteract scoring and ended by a PTMProphet analysis.

My issue is the following : PTMProphet fails to initializes from the interact.pep.xml input file due to "Unrecognized mod c[17] on peptides" (see screenshot 1).

This modification corresponding to the "cleavage C-terminal mass change" parameters of X!Tandem database search. I tried to set this modification in PTMProphet parameters but it didn't work better (see screenshot 2). I also tried to delete this parameter in X!Tandem database search and not surprisingly almost all my target proteins were not identified. But PTMProphet worked without issue in this configuration so this parameter really seems to be the key. 

Any idea to get out of this issue?

Many thanks in advance!

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