Hi David, My dataset is of N-terminal dimethyl labelled peptides (also natural acetylated N-terminal peptides included in the mix..) analysed on an LTQ-Orbitrap. I am new searching against a database (Mouse IPI v3.87) containing decoys and have now been using the PeptideProphet option ' Only use Expect Score as the discriminant - helpful for data with homologous top hits, e.g. phospho or glyco (Tandem only) '. Both of these have improved my models for +3 and +4 but the model for +2 is still poor.
I've had the same dataset analysed on LTQ-Orbitrap using ETD for >+3 charge and modelling in TPP looks great for >+3 charge data but is still poor for +2 charge. I've attached example of X!Tandem parameter file that I'm currently using for searches. Any suggestions on how I can improve modelling for +2 charge would be great. Thanks, Claire On Tuesday, 18 September 2012 00:14:44 UTC+9:30, David Shteynberg wrote: > > Unfortunately your "good" spectra scores overlap significantly with you > bad spectrum scores. So PeptideProphet has trouble classifying this > dataset. Can you tell us more about your dataset and the search > parameters used? Does your database contain any decoys? > > Thanks, > David > On Sep 16, 2012 7:57 PM, "Claire" <[email protected] <javascript:>> > wrote: > >> Hi Bjorn, >> >> Did you ever get a solution to this problem? >> >> I keep encountering the same issue. >> >> Thanks, >> >> Claire >> >> On Friday, August 27, 2010 1:23:54 AM UTC+9:30, Bjorn wrote: >>> >>> Hi, >>> >>> I can do a tandem database search that results in a .tandem file. >>> I successfully convert it into a .tandem.pep.xml where I clearly see >>> that I have 2+ and 3+ spectra with hyperscores of +700. >>> When I run peptideprophet on that file, the result is a .pep.xml file >>> with only the 1+ left (no 2+ or 3+) >>> Where have all the good spectra I had before Xinteract gone?? >>> I would expect those to be still there and have high probability >>> scores... >>> >>> Any suggestion is welcome. >>> >>> I'm using TPP 4.4.0 on Mac OS X 10.6.4. >>> >>> Bjorn >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To view this discussion on the web visit >> https://groups.google.com/d/msg/spctools-discuss/-/WFHXaitAt_4J. >> To post to this group, send email to >> [email protected]<javascript:> >> . >> To unsubscribe from this group, send email to >> [email protected] <javascript:>. >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/cYeLEInZlCUJ. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
Input_Heavy_DiMet.xml
Description: XML document
