No.  It uses the top hit only.

On Tue, Apr 4, 2017 at 7:34 AM, Chih-Chiang Tsou <chihchiang.t...@gmail.com>
wrote:

> Hi
>
> Is there any option in xinteract to tell PeptideProphet take topN hits for
> each spectrum for probability calculation?
>
> Thanks,
> Chih-Chiang
>
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