Dear Jimmy
Thanks for your reply. I will use the correct database.
Felipe
El jue, 4 may 2023 a las 15:30, Jimmy Eng () escribió:
> Felipe,
>
> You should not search sequence databases composed of just a single protein
> or even tens of proteins and hope to process them through downstream
>
Felipe,
You should not search sequence databases composed of just a single protein
or even tens of proteins and hope to process them through downstream
validation tools like the Prophets. When you do this, you break lots of
assumptions that the tools expect which makes the results, like
Hello Luis
Thanks for your request. Yes, I performed TPP/Prophets, and their
probability is high as 0.9 or 1, in many peptides. The database I used
only contains my protein of interest in FASTA. I do not know how to use
decoys.
Kind regards,
Felipe
El mar, 2 may 2023 a las 22:53, 'Luis
Hello Felipe,
There may be several reasons why you see the viral protein in your
analysis, e.g.
- Did you only run Comet, or did you validate using the TPP/Prophets?
If the latter, what was the probability of the protein(s) in question?
- What were the contents of the database that you
Hello
I have a question about protein validation. I am trying to use TPP to
identify post-translational modifications of certain proteins. I performed
a Comet search using the sequence of my protein of interest. However, while
exploring another database, I performed a search using a protein that
