Thanks David! On Tuesday, September 20, 2016 at 10:52:12 PM UTC-4, David Shteynberg wrote: > > 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] <javascript:>> > 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] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> Visit this group at https://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > >
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