Hi Jason, Thank you for your answer. I just want to assure myself - is it possible to do this like selecting two or more files (pep.xml after a tandem search) in TPP with the selection of one interact.pep.xml output file? Since I use the Windows TPP this would be the best way if it is ok. I appreciate your help, thanks. Pavel
the procedure you wrote the same Dne pátek, 1. března 2013 17:51:05 UTC+1 Jason Winget napsal(a): > > Hi Pavel, > I believe that the way to merge data is as follows: > > 1. Merge the pep.xml results (from a single search engine) using > InteractParser into an "interact.pep.xml" > 2. Run RefreshParser on the interact.pep.xml > 3. Continue the TPP pipeline (PeptideProphet, iProphet, > ProteinProphet) on the interact.pep.xml > > This should work for either technical replicates or fractionated samples. > Alternatively I believe the xinteract command will handle a lot of this > for you. Run xinteract (from the command line) without arguments for a > comprehensive usage statement. > > You can also get more information here: > > http://tools.proteomecenter.org/wiki/index.php?title=TPP:Developer_Documentation#Running_the_TPP > > Best, > Jason > > On Thursday, February 28, 2013 1:26:18 PM UTC-8, Pavel wrote: >> >> Dear all, >> >> I would like to ask a couple of questions about replicate data processing. >> I appreciate any comments on this topic. >> >> 1. What is the best step to „merge data“ for technical replicates in TPP? >> For example, I have 5 runs of the same sample (to identify as much >> proteins/peptides as possible) and searched each file against database. >> Do I have to select all the files for PeptideProphet analysis and thus >> merge them to one pep.xml file? Or do I have to analyse each file >> separately and select the five pep.xml files in ProteinProphet with >> exporting to one prot.xml file? I tried both the ways and the results >> differed just a bit (only probability values, not proteins identified) >> which I guess is due to the different number of spectra/peptides used in >> the analysis. I just wonder what is the best way from the statistical point >> of view. >> >> 2. The same question as above but when one deals with fractions of the >> same sample (e.g., SCX fractions). What is the step in TPP to „merge data“? >> >> 3. And what about the combination of fractions and technical replicates? >> >> Thanks for your comments, >> >> Pavel >> >> PS: I would like to thank the authors of TPP, I have finally installed it >> and have to say it is an amazing software. >> > -- 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. Visit this group at http://groups.google.com/group/spctools-discuss?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
