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 -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
