1.You can refer to the MCP paper about iProphet. Here is the link: http://www.mcponline.org/content/10/12/M111.007690.long. 2. SpectraST can create a consensus library by removing the redundant spectra. SpectraST can handle more than 225,000 spectra, and I used SpectraST to process much more than that number of spectra. 3. Combining pep.xml with iProphet and then creating a library with SpectraST is better.
On Tue, Sep 20, 2016 at 3:26 AM, Ali <[email protected]> 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 > > -- > 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. > -- 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.
