Dear list, I am trying to incorporate multiple database search engines and iProphet into my data analysis. I run the TPP from commandline with following commands:
1) For single search engines (here: X!Tandem): xinteract -Ninteract_xtandem.pep.xml -p0.05 -l7 -OARP -dSHUFFLED -X-m0.02-nK,6.031817-nn,6.031817-H *.pep.xml ProteinProphet interact_xtandem.pep.xml interact_xtandem.prot.xml XPRESS EXCLUDE_ZEROS 2) To use iProphet on this single database search engines: xinteract -Ninteract_xtandem.pep.xml -p0.05 -l7 -OARP -dSHUFFLED -X-m0.02-nK,6.031817-nn,6.031817-H *.pep.xml c:\Inetpub\tpp-bin\InterProphetParser \Xtandem\interact_xtandem.pep.xml interact.ipro.pep.xml ProteinProphet interact.ipro.pep.xml interact_xtandem.ipro.prot.xml XPRESS EXCLUDE_ZEROS IPROPHET 3) For multiple search engines (here: X!Tandem and MSGF+): c:\Inetpub\tpp-bin\InterProphetParser \Xtandem\interact_xtandem.pep.xml \MSGF\interact_msgf.pep.xml interact.ipro.pep.xml RefreshParser interact.ipro.pep.xml %dbase% ProteinProphet interact.ipro.pep.xml interact_ipro.prot.xml XPRESS EXCLUDE_ZEROS IPROPHET 4) For testing, I also ran ProteinProphet on the combined iProphet output without using the IPROPHET option: c:\Inetpub\tpp-bin\InterProphetParser \Xtandem\interact_xtandem.pep.xml \MSGF\interact_msgf.pep.xml interact.ipro.pep.xml RefreshParser interact.ipro.pep.xml %dbase% ProteinProphet interact.ipro.pep.xml interact_ipro.prot.xml XPRESS EXCLUDE_ZEROS In an example analysis, I identified the following number of Proteins after using <1% FDR based on the ProteinProphet estimation: 1a) X!Tandem only: 3,657 Proteins (589 single hits) 1b) MSGF+ only: 3,791 Proteins (614 single hits) 2a) X!Tandem with iProphet: 3,325 (735 single hits) 2b) MSGF+ with iProphet: 3,473 Proteins (773 single hits) 3) X!Tandem, MSGF+ and iProphet: 3,803 Proteins (964 single hits) 4) X!Tandem, MSGF+ without IPROPHET option: 4,220 proteins (732 single hits) It seems like iProphet reduces the number of protein IDs, while increasing the single hits. So, if I substract the single hits, I even get less protein IDs when using two database search engines instead of one. It even gets worse when I use Myrimatch together with X!Tandem and MSGF+. How can that be? Did I do some obvious mistake here? Or do I have to switch off single models of the iProphet? If not, is it acceptable to use iProphet output without the IPROPHET option in ProteinProphet? This way, I can use multiple search engines and INCREASE my IDs, instead of loosing some. Many thanks! -- 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. For more options, visit https://groups.google.com/d/optout.
