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:
On Tue, Sep 20, 2016 at 10:44 AM, Ali <sma.banijam...@gmail.com> wrote:
> 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,
> 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:
>> 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 <sma.ban...@gmail.com> wrote:
>>> 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,
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