You don't need to run ProteinProphet to create a library.  Run SpectraST to
create a consensus library, it will use all spectra matching a given
peptide and passing your threshold to create on consensus library spectrum
for that peptide.   The SpectraST wiki page has all the details:
http://tools.proteomecenter.org/wiki/index.php?title=Software:SpectraST#SpectraST_Create_Mode

-David

On Tue, Sep 20, 2016 at 2:42 PM, Ali <sma.banijam...@gmail.com> wrote:

> Thanks David very helpful! Everything is much more clear now. So now I
> just have one more question:
>
> My ultimate goal is to create a spectral library from all these results.
> If I understood correctly, I should now take the pep.xml file processed
> with iprophet (which contains similar peptides of different spectra) and
> process it with ProteinProphet (with the IPROPHET option on), and then
> create a spectral library from the resulting file?
>
> Is this a better approach comparing with creating a consensus library from
> individual search results (each processed with PepPro and iPro) with
> SpectraST?
>
> Thank you very much.
>
> On Tuesday, September 20, 2016 at 3:35:34 PM UTC-4, David Shteynberg wrote:
>>
>> Ali,
>>
>> iProphet will compute a probability of each unique spectrum separately.
>> It only combines PSM if they represent repeated searches of the same
>> spectrum.  For example, if the spectrum was searched multiple times with
>> different searches.  If you want the probability of a particular peptide
>> you must take all spectra matching that peptide and take the maximum
>> probability of those.  ProteinProphet will do this for you when run with
>> IPROPHET input and option enabled.  It will go further and assemble these
>> peptides into proteins (and compute probabilities) observed in the sample.
>>
>>
>> -David
>>
>> On Sep 20, 2016 6:32 AM, "Ali" <sma.ban...@gmail.com> wrote:
>>
>>> Sorry I made a mistake here! I am getting similar *peptides*! Not
>>> *spectra*!
>>>
>>> On Monday, September 19, 2016 at 3:26:20 PM UTC-4, Ali 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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