Thanks David!

On Tuesday, September 20, 2016 at 10:52:12 PM UTC-4, David Shteynberg wrote:
>
> You don't need to run ProteinProphet to create a library.  Run SpectraST 
> to create a consensus library, it will use all spectra matching a given 
> peptide and passing your threshold to create on consensus library spectrum 
> for that peptide.   The SpectraST wiki page has all the details: 
> http://tools.proteomecenter.org/wiki/index.php?title=Software:SpectraST#SpectraST_Create_Mode
>
> -David
>
> On Tue, Sep 20, 2016 at 2:42 PM, Ali <sma.ban...@gmail.com <javascript:>> 
> wrote:
>
>> Thanks David very helpful! Everything is much more clear now. So now I 
>> just have one more question:
>>
>> My ultimate goal is to create a spectral library from all these results. 
>> If I understood correctly, I should now take the pep.xml file processed 
>> with iprophet (which contains similar peptides of different spectra) and 
>> process it with ProteinProphet (with the IPROPHET option on), and then 
>> create a spectral library from the resulting file?
>>
>> Is this a better approach comparing with creating a consensus library 
>> from individual search results (each processed with PepPro and iPro) with 
>> SpectraST?
>>
>> Thank you very much.
>>
>> On Tuesday, September 20, 2016 at 3:35:34 PM UTC-4, David Shteynberg 
>> wrote:
>>>
>>> Ali,
>>>
>>> iProphet will compute a probability of each unique spectrum separately.  
>>> It only combines PSM if they represent repeated searches of the same 
>>> spectrum.  For example, if the spectrum was searched multiple times with 
>>> different searches.  If you want the probability of a particular peptide 
>>> you must take all spectra matching that peptide and take the maximum 
>>> probability of those.  ProteinProphet will do this for you when run with 
>>> IPROPHET input and option enabled.  It will go further and assemble these 
>>> peptides into proteins (and compute probabilities) observed in the sample.
>>>
>>>
>>> -David
>>>
>>> On Sep 20, 2016 6:32 AM, "Ali" <sma.ban...@gmail.com> wrote:
>>>
>>>> Sorry I made a mistake here! I am getting similar *peptides*! Not 
>>>> *spectra*!
>>>>
>>>> On Monday, September 19, 2016 at 3:26:20 PM UTC-4, Ali 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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