1.You can refer to the MCP paper about iProphet. Here is the link:
http://www.mcponline.org/content/10/12/M111.007690.long.
2. SpectraST can create a consensus library by removing the redundant
spectra. SpectraST can handle more than 225,000 spectra, and I used
SpectraST to process much more than that number of spectra.
3. Combining pep.xml with iProphet and then creating a library with
SpectraST is better.

On Tue, Sep 20, 2016 at 3:26 AM, Ali <sma.banijam...@gmail.com> wrote:

> Hello
>
> I am combining multiple search results (all from X!Tandem) using iprophet
> to then make a spectral library of them with SpectraST. I have some
> questions:
>
> 1. What is the iprophet probability, What does it show and How does it
> combine search results? I want to know how it is calculated to be able to
> set a reasonable threshold for the results to include them in the spectral
> library. Can someone kindly explain iprophet for me.
>
> 2. I am getting many similar spectra (and naturally with different
> iprobabilities because they are for different searches) in the result of
> combination of my search results (using iprophet). How can I remove these
> similar spectra? or avoid recording them in the first place? The problem is
> that I am having a very large combination-file with more than 225,000
> spectra which then SpectraST has issues handling it. Isn't iprophet
> supposed to avoid recording identical spectra while combining results?
>
> 3. As I said, I combined individual files (each processed with
> PeptideProphet and iProphet) with iprophet and then created a spectral
> library from the final file, but there is another approach which is making
> individual spectral libraries and then creating a consensus library form
> them using SpectraST. I wanted to know which one is the better approach:
> Combining pep.xml's using iprophet and then creating a library OR making
> individual libraries and then making a consensus library from those
> individual libraries.
>
> Thank you very much for your time,
>
> Ali
>
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