> From: [email protected] [mailto:spctools-
> [email protected]] On Behalf Of [email protected]
>
> Greetings all--
>
> The enhancements in new versions are great!  But where can I find more
> information on the ProteinProphet confidence calculation--what goes
> into it and how to interpret it? The release notes indicate it is
> based on a States et al. -like algorithm--is there a reference for
> this, or perhaps States's initials and approximate date of
> publication?

States et al. (2006) Nature Biotech. 24(3):333-338

> And, in  PeptideProphet results, what is the difference between
> peptides and stripped peptides?

Stripped peptides means irrespective of any modifications. i.e. all mass
modifications have been "stripped" out.

Regards,
Eric


> Thanks
>
> Mary

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