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]> 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]. > 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.
