Re: [spctools-discuss] Re: Question About iprophet/Spectral library

2016-09-20 Thread Ali 
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  
> 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"  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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Re: [spctools-discuss] Re: Question About iprophet/Spectral library

2016-09-20 Thread Ali 
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"  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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>

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Re: [spctools-discuss] Re: Question About iprophet/Spectral library

2016-09-20 Thread David Shteynberg 
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"  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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