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/**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]. > 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. > > > -- 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.
