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:* [email protected] <javascript:> [mailto: > [email protected] <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 <[email protected] <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 <[email protected]> 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 [email protected]. > To post to this group, send email to [email protected]. > 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 [email protected] <javascript:>. > To post to this group, send email to [email protected] > <javascript:>. > 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 [email protected] <javascript:>. > To post to this group, send email to [email protected] > <javascript:>. > 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. 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