Thanks for you answer. I want to make sure my calculation is correct. The details of protein prophet result is -
*Minimum probability**Sensitivity**Error rate*0.001.00000.89600.101.0000 0.23900.201.00000.23900.300.96700.17800.400.94100.14600.500.90700.11700.60 0.86300.08900.700.80800.06400.800.73900.04200.900.62900.02100.950.52100.0090 0.960.50100.00700.970.47400.00600.980.41300.00300.990.36900.00101.000.0860 0.0000 Based on this result, what is probability cutoff that gives me 1% FDR? Thanks Sandeep On Friday, March 15, 2013 11:01:24 AM UTC-5, kshitiz wrote: > > Sorry I probably was not clear enough. Number of unique peptides for a > protein are actually number of PSMs, so hypothetically if a protein was > identified based on one peptide that was fragmented 10 times and 8 out of > those 10 ms/ms spectra result in peptide spectrum match , then number of > unique peptides will read 8 however you have identified only one peptide. > > I hope someone on the forum can correct me if I am wrong. > > Additionally, you said that you filter at p > 0.9, this is not very > informative and not the best way of filtering. Instead you should filter at > a p value that controls for less than 1% FDR. > > cheers > > > On Fri, Mar 15, 2013 at 3:05 PM, Sandeep <[email protected]<javascript:> > > wrote: > >> Hello, >> >> Sorry, I think I did not understand your answer. My concern was- why I >> have more number of unique peptides as compared to TOTAL number of peptides >> in my data after protein prophet grouping and filtering my data to contain >> only groups with probability more than 0.9. >> >> Thanks >> >> Sandeep >> >> >> >> >> On Friday, March 15, 2013 3:41:11 AM UTC-5, kshitiz wrote: >>> >>> Hi, >>> I think the number given under number of unique peptides is actually >>> number of unique PSMs used for the identity of that protein. If you want >>> actual number of unique peptides then you will have to pull the data into >>> an SQL based server and then query it to to count distinct peptides for >>> each protein. >>> >>> cheers. >>> >>> >>> On Thu, Mar 14, 2013 at 10:00 PM, Sandeep <[email protected]> wrote: >>> >>>> Hi, >>>> >>>> I have recently started using peptide/proteinprophet. I noticed that in >>>> my data, there are several protein groups for which the number of unique >>>> peptidees is more than the number of total peptides (mostly the total >>>> number of peptides is 0). Is this data reliable? How to explain this. >>>> Thanks in advance for any answers. >>>> >>>> Sandeep >>>> >>>> >>>> >>>> -- >>>> 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 spctools-discu...@**googlegroups.com. >>>> To post to this group, send email to spctools...@googlegroups.**com. >>>> Visit this group at http://groups.google.com/** >>>> group/spctools-discuss?hl=en<http://groups.google.com/group/spctools-discuss?hl=en> >>>> . >>>> For more options, visit >>>> https://groups.google.com/**groups/opt_out<https://groups.google.com/groups/opt_out> >>>> . >>>> >>>> >>>> >>> >>> >>> >>> -- >>> Kshitiz Tyagi >>> >>> -- >> 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] <javascript:>. >> To post to this group, send email to >> [email protected]<javascript:> >> . >> Visit this group at http://groups.google.com/group/spctools-discuss?hl=en >> . >> For more options, visit https://groups.google.com/groups/opt_out. >> >> >> > > > > -- > Kshitiz Tyagi > > -- 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?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
