Thanks again! I will look into it. On Monday, September 19, 2016 at 11:02:10 PM UTC-4, andyzcq wrote: > > I have never done the SpectraST search. > When you create a consensus library using SpectraST, you actually removed > redundant spectra. You can refer to Nature method paper about SpectraST. > Here is the link: > http://www.nature.com/nmeth/journal/v5/n10/full/nmeth.1254.html > > On Tue, Sep 20, 2016 at 10:44 AM, Ali <[email protected] <javascript:>> > wrote: > >> Hi >> >> Thanks so much for your answers! >> >> I created a library with Spectrast once without error but when I wanted >> to do a spectral search with it, I got an error saying the library is >> corrupt and when I tried to create the same library again, I received error >> each time at different points during the creation process. I noticed that >> some other people had this issue on Windows, but I am creating the library >> on a cluster using Linux. I thought the issue might be due to the size of >> the library. The library is more than 4 gbs. But then I noticed that the >> combination of results which I created using iprophet (and then used to >> create the spectral library) has many redundant spectra. Could you please >> tell me what should I do exactly to remove those redundant spectra? >> >> Or, what are the correct steps that I should take to make a spectral >> library from a pep.xml created with iprophet which contains all of the >> search results (and redundant spectra as well), to make sure that there is >> no redundant spectra in the library? >> >> Thanks again, >> >> Ali >> >> I >> >> On Monday, September 19, 2016 at 9:35:47 PM UTC-4, andyzcq wrote: >>> >>> 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] <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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