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