Thanks so much. Editing the files fixed the error. Our mass spec is supposed to be filtering out charge states that high, but I guess it isn't.
-Dennis On Thu, Oct 13, 2011 at 5:28 PM, David Shteynberg < [email protected]> wrote: > Hi Dennis, > > Thanks for uploading your dataset. It appears that the source of the > problem here is scan number 32376 in the mzXML and pep.xml file. This > spectrum happens to be charge 10 (the only one of this charge found in the > data). PeptideProphet models charges 1 through 7 only and incorrectly > interprets this spectrum as charge one instead of charge 10. Do resolve > this issue please delete the spectrum_query entry for this spectru from the > pep.xml file. > > -David > On Oct 8, 2011 6:56 PM, "Dennis Goldfarb" <[email protected]> > wrote: > >> I uploaded an example dataset with this issue. It is in >> /incoming/MAJOR_LAB_UNC_MA145.zip >> >> On Mon, Oct 3, 2011 at 6:27 PM, SPCTools Admin <[email protected]>wrote: >> >>> Hi Dennis, >>> >>> This should not happen and it indicates a problem with running the >>> algorithm on your dataset. Do you still see the message when you >>> disable the option to force the distribution fit? This is an option >>> that should be used for troubleshooting only and is not expected to >>> generate good results. If you can package the dataset and post to our >>> FTP server I can debug the issue further. Instructions for posting >>> data to FTP can be found here: >>> >>> http://tools.proteomecenter.org/wiki/index.php?title=TPP:Frequently_Asked_Questions#How_do_I_upload_files_to_the_SPC_tools_team.3F >>> >>> -David >>> >>> >>> >>> On Oct 3, 8:49 am, Dennis Goldfarb <[email protected]> wrote: >>> > Hi, >>> > >>> > Every once in a while I receive an error stating: >>> > >>> > Iterations: .Assertion failed: idx < posProbs_->size(), file >>> > Validation/InterProphet/InterProphetParser/KDModel.cxx, line 143 >>> > >>> > As far as I can tell this means that there aren't enough likely true >>> spectra >>> > to properly model the true and false distributions. Is this the correct >>> way >>> > to interpret the error? In the past I've only seen it when the # of >>> decoy >>> > hits is almost the same as forward hits, so that makes sense to me. >>> Lately >>> > I've had this error pop up when there are thousands more forward hits >>> than >>> > decoys, but only if I use the accurate mass binning model. The program >>> > executes fine and the results look great (3000+ peptides of bait) >>> without >>> > accurate mass binning. We have an orbitrap and I haven't had this issue >>> in >>> > the past. Could this be a sign that our instrument's accuracy is >>> slipping >>> > and needs reconfiguration/maintenance? Could someone give me an idea of >>> how >>> > severely the accurate mass binning model penalizes the mass difference? >>> > >>> > I'm using TPP v4.5.0 on a Windows 7 Machine. I've tried combinations of >>> > forcing the distribution fit, and using non-parametric distributions. >>> > >>> > Thank you, >>> > >>> > -- >>> > Dennis Goldfarb >>> > Graduate Student >>> > Department of Computer Science >>> > University of North Carolina at Chapel Hill >>> >>> -- >>> You received this message because you are subscribed to the Google Groups >>> "spctools-discuss" group. >>> 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. >>> >>> >> >> >> -- >> Dennis Goldfarb >> Graduate Student >> Department of Computer Science >> University of North Carolina at Chapel Hill >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> 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. >> > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > 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. > -- Dennis Goldfarb Graduate Student Department of Computer Science University of North Carolina at Chapel Hill -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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.
