Thanks David very helpful! Everything is much more clear now. So now I just have one more question:
My ultimate goal is to create a spectral library from all these results. If I understood correctly, I should now take the pep.xml file processed with iprophet (which contains similar peptides of different spectra) and process it with ProteinProphet (with the IPROPHET option on), and then create a spectral library from the resulting file? Is this a better approach comparing with creating a consensus library from individual search results (each processed with PepPro and iPro) with SpectraST? Thank you very much. On Tuesday, September 20, 2016 at 3:35:34 PM UTC-4, David Shteynberg wrote: > > Ali, > > iProphet will compute a probability of each unique spectrum separately. > It only combines PSM if they represent repeated searches of the same > spectrum. For example, if the spectrum was searched multiple times with > different searches. If you want the probability of a particular peptide > you must take all spectra matching that peptide and take the maximum > probability of those. ProteinProphet will do this for you when run with > IPROPHET input and option enabled. It will go further and assemble these > peptides into proteins (and compute probabilities) observed in the sample. > > > -David > > On Sep 20, 2016 6:32 AM, "Ali" <sma.ban...@gmail.com <javascript:>> wrote: > >> 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 >>> >> -- >> 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 spctools-discu...@googlegroups.com <javascript:>. >> To post to this group, send email to spctools...@googlegroups.com >> <javascript:>. >> 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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
