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.banijam...@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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