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
Thank you very much for your time,
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