Hi Eric

Thanks for your reply.

I am using the SpectraST on a cluster with Linux.

This is the the version that I am working with:

SpectraST (version 5.0, TPP v4.8.0 PHILAE, Build 201608051257-exported 
(RedHatEnterpriseServer-x86_64)) by Henry Lam.

By the way I noticed that I made a mistake in my previous posts, I am 
getting similar *peptides* (not *spectra*) in the result of combining 
several search results with iprophet. Do you have a solution for avoiding 
redundant peptides when combining multiple search results with iprophet? I 
think these similar identified peptides are making my library larger than 
it should be.

Many Thanks,

Ali



On Tuesday, September 20, 2016 at 3:15:13 AM UTC-4, Eric Deutsch wrote:
>
> I suspect the problem is that an old 32-bit version of SpectraST will 
> create a corrupt index for any library larger than 2 GB. The library splib 
> file is fine, but the index will be corrupt and a search using that library 
> will not work.
>
>  
>
> The solution is to use a version of SpectraST compiled for a 64-bit 
> operating system, both to create the library and to search with the library.
>
>  
>
> What operating system are you running with, is this Windows or Linux? Is 
> your operating system 64-bit?
>
>  
>
> Regards,
>
> Eric
>
>  
>
>  
>
> *From:* spctools...@googlegroups.com <javascript:> [mailto:
> spctools...@googlegroups.com <javascript:>] *On Behalf Of *???
> *Sent:* Monday, September 19, 2016 8:02 PM
> *To:* spctools-discuss@googlegroups com
> *Subject:* Re: [spctools-discuss] Question About iprophet/Spectral library
>
>  
>
> 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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