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-discuss@googlegroups.com [mailto: spctools-discuss@googlegroups.com] *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.banijam...@gmail.com> 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 -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discu...@googlegroups.com. To post to this group, send email to spctools...@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. 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