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 

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,


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