Hi Julia, Certainly it is possible that those are false IDs, but it depends as it often does on other factors.
Did you find other confidently IDed peptides that are not Phosphorylated? What is the relative sizes of the positive and negative mixture distributions in the data? Do you expect that most of your correct peptides are phosphorylated? You can try to enable the PeptideProphet option "Leave alone all entries with asterisked score values", which is often helpful in these situations where you would expect many homologous top matches due to phosph-site uncertainty. However, if that doesn't help your situation, the there maybe other potential points of failure to identify phospho peptides in this approach. If you need further help, please compress your data (and database) into one zip file and then post it somewhere we can download and look at it (e.g. http://tools.proteomecenter.org/wiki/index.php?title=TPP:Frequently_Asked_Questions#How_do_I_upload_files_to_the_SPC_tools_team.3F) Thank you, -David On Fri, Oct 21, 2011 at 12:08 PM, [email protected] <[email protected]> wrote: > Hey Guys, > > I have a question regarding identification of phosphopeptide using > TPP. I got a data using an LTQ-XL (using CID) and I ‘ve searched using > MASCOT search engine (phosphorylation as a variable modification in S/ > T/Y) . I found more than 50 phosphorylated proteins however when I > use TPP to look at these phosphorylations I found none! I am wondering > if all the phoshphorylation detected by MASCOT are in fact false > positives. > Here is what I’ve done: > I use TPP v4.4 rev 1 in W7 > Run MASCOT > Convert *.dat to *.pepxml > Run PeptideProphet (I’ve selected the icon “Use phospho information”) > and ProteinProphet afterwards. > Can anyone help me? > Thanks in advance! > > Julia > > -- > 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.
