Great! Although when you set MINPROB=0 the software is spending a lot of
time evaluating PSMs you will never use, and some of them might have many
mods causing a combinatorial expansion of peptide candidates the must be
evaluated (although this is less of an issue for MASSDIFFMODE.) If you set
thi
Hi David,
Using MINPROB=0 solved this problem. Thanks!
Alex
On Monday, April 6, 2020 at 4:11:47 PM UTC-7, David Shteynberg wrote:
>
> 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
