You don't need to run ProteinProphet to create a library. Run SpectraST to create a consensus library, it will use all spectra matching a given peptide and passing your threshold to create on consensus library spectrum for that peptide. The SpectraST wiki page has all the details: http://tools.proteomecenter.org/wiki/index.php?title=Software:SpectraST#SpectraST_Create_Mode
-David On Tue, Sep 20, 2016 at 2:42 PM, Ali <[email protected]> wrote: > 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" <[email protected]> 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 [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. > -- 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.
