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 [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
