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 <sma.ban...@gmail.com <javascript:>> 
> 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
>>
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