Hello Vijay, Force fitting the models is not recommended. PeptideProphet usually does a good job at selecting out the bad models and in your data a great majority of the hits matched decoys suggesting either wrong search settings or database or bad quality data. You need to troubleshoot your analysis upstream of PeptideProphet/iProphet.
David On Tue, Jun 21, 2016 at 12:57 PM, Vijay Kumar <[email protected]> wrote: > Hi, > Yes, when i am selecting Force the fitting of the mixture model (bypass > automatic mixture model checks) option i succeeded peptideprophet and > iprophet. > > On Sunday, June 19, 2016 at 7:37:20 AM UTC+5:30, andyzcq wrote: >> >> I guess the developers of TPP are TOO busy to respond to you. >> >> Similarly, no one repond to my question concerning PTMprophet. >> >> Have you succeeded to run peptideprophet and iprophet? >> >> On Sun, Jun 19, 2016 at 2:47 AM, Vijay Kumar <[email protected]> wrote: >> >>> Hi, >>> Where i will get the complete step wise tutorial for Decoy peptide and >>> protein validation including Mayu procedure for TPP. >>> >>> -- >>> 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 https://groups.google.com/group/spctools-discuss. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> -- > 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 https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- 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 https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
