Thanks a lot Kshitiz for your prompt replies and helping me. I have a one more question, when you run protein prophet to get the protein groups with 1% FDR cutoff, do you ALSO use peptides with 1% FDR cutoff for the protein assignments?
Thanks Sandeep On Wednesday, March 20, 2013 12:14:34 PM UTC-5, kshitiz wrote: > > p value for this example should be just under .95, p value of 0.9 that you > were using will give you 2.1% FDR. I almost always run MAYU on my results > and that tells the p Value corresponding to 1% FDR at protein level. > > > On Wed, Mar 20, 2013 at 3:40 PM, Sandeep <[email protected]<javascript:> > > wrote: > >> 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*0.00 1.00000.89600.101.0000 >> 0.23900.201.00000.23900.300.96700.17800.400.9410 0.14600.500.90700.1170 >> 0.600.86300.08900.700.80800.06400.800.73900.0420 0.900.62900.02100.95 >> 0.52100.00900.960.50100.00700.970.47400.00600.98 0.41300.00300.990.3690 >> 0.00101.000.08600.0000 >> >> >> 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]> 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/**grou**ps/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 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. 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