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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