Thanks David!
On Tuesday, September 20, 2016 at 10:52:12 PM UTC-4, David Shteynberg wrote:
>
> You don't need to run ProteinProphet to create a library. Run SpectraST
> to create a consensus library, it will use all spectra matching a given
> peptide and passing your threshold to create on cons
You don't need to run ProteinProphet to create a library. Run SpectraST to
create a consensus library, it will use all spectra matching a given
peptide and passing your threshold to create on consensus library spectrum
for that peptide. The SpectraST wiki page has all the details:
http://tools.p
Thanks David very helpful! Everything is much more clear now. So now I just
have one more question:
My ultimate goal is to create a spectral library from all these results. If
I understood correctly, I should now take the pep.xml file processed with
iprophet (which contains similar peptides of
Ali,
iProphet will compute a probability of each unique spectrum separately. It
only combines PSM if they represent repeated searches of the same
spectrum. For example, if the spectrum was searched multiple times with
different searches. If you want the probability of a particular peptide
you m
Sorry I made a mistake here! I am getting similar *peptides*! Not *spectra*!
On Monday, September 19, 2016 at 3:26:20 PM UTC-4, Ali wrote:
>
> Hello
>
> I am combining multiple search results (all from X!Tandem) using iprophet
> to then make a spectral library of them with SpectraST. I have some
