Hi Alex,
PTMProphet by default will ignore any spectrum with less than 90%
probability (iProphet is used when available.) You can change this by
setting the option MINPROB= when you run the tool. Let me know if that
still fails for you.
Thanks,
-David
On Mon, Apr 6, 2020 at 3:27 PM Alex Zelt
I am running into a situation where MSFragger returns a massdiff but
PTMProphet seems to ignore it. No modification_info or mod_aminoacid_mass
position is reported by PTMProphet for some results, while for others
things work as expected.
Here are 2 PSMs as examples. I've included both MSFragger
I think you found a bug. There is some rare property of a particular
precursor scan in that file that Kojak isn't handling correctly. I'll
probably need access to that particular mzML file to identify the bug. I'll
reach out to you by email.
On Monday, April 6, 2020 at 12:39:33 PM UTC-7, Lindse
The screenshot shows all that's in the command-line output sub-window. It
stops while mapping precursors and gives no further diagnostic messages.
Any reasons it would stop running?
On Monday, March 30, 2020 at 1:33:18 PM UTC-7, Luis wrote:
>
> Hi Lindsey,
>
> It seems that Kojak did not finish
