*hi, dear TPP team,* *I got a set of 3-plex dimethylated LC-MSMS data and wish to use ASAPratio to get the quantitation data. However, the parameter input of ASAPratio is not really that straightforward, and I have tried several times but all with error message.* *Here is what I have done: all pepitdes were carbamidomethylated, and then the K is blocked by +42 (guandination). then three set of sample were labeled by dimethylation (+28, 32, 36) at N term, then pooled for LCMSMS. I have used both Comet and Tandem to search the database, and have successfully used iprophet to combined the results from both engines. *
*Now I read some posts here suggesting to search data separately for each dimethylation label. Therefore, for Comet and Tandem searches, each time I set one dimethylated Nterm as static modification, and at end I have 3 separate sets of ipro.pep.xml files. * *I understand that ASAPratio can only handle 2plex data, so I start with one pair (L+H), and set the following parameter:* c:\Inetpub\tpp-bin\InterProphetParser c:/Inetpub/wwwroot/ISB/data/Comet_tandem_L.ipro.pep.xml c:/Inetpub/wwwroot/ISB/data/comet_tandem_H.ipro.pep.xml Comet_tandem_LH.ipro.pep.xml&c:\Inetpub\tpp-bin\ASAPRatioPeptideParser interact.ipro.pep.xml -ln -r0.05 -i0.5 -S -mM131.04049K170.11497C160.03019 *the xinteractor failed with this message:* *error: *cannot have variable modified n in static mode *then I tried:* c:\Inetpub\tpp-bin\InterProphetParser c:/Inetpub/wwwroot/ISB/data/Comet_tandem_L.ipro.pep.xml c:/Inetpub/wwwroot/ISB/data/comet_tandem_H.ipro.pep.xml Comet_tandem_LH.ipro.pep.xml&c:\Inetpub\tpp-bin\ASAPRatioPeptideParser interact.ipro.pep.xml -ln -r0.05 -i0.5 -S -mM147.035K170.11497C160.03019n29.03n37.0757 *still got the same error message:* *error*: cannot have variable modified n in static mode *Anyone knows how to set up the ASAPratio for this scenario? You help is really appreciated! * *In addition, I also searched the data using +28 as the static mod and +4, +8 as variable mods at Nterm. I'm interested to see how separate search results differ from search with all modifications. In this case, how shall I set up the ASAPratio? * *Thank you very much! * SunSun -- 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.
