Yes your understanding of the issue is spot on. iProphet converts
everything to L for comparison, then reports the top hit from the highest
scoring search engine as reported by the search engine. Post processing
has to take care of how to treat the variants.
Cheers,
-David
On Tue, Jun 12, 2018
Hi David,
Thank you for the quick reply. The three search engines I am using they
rank I/L variant peptides inconsistently. Some ranks Leucine-version as
rank 1, some ranks Isoleucine-version as rank 1.
Then in iProphet pepXML file I observed that for each spectrum iProphet
picks rank 1 hit info
Hello Chih-Chiang,
iProphet will convert all Isoleucines reported to Leucines for comparison
purposes. Have you observed an error in your analyses?
-David
On Tue, Jun 12, 2018 at 9:06 AM, Chih-Chiang Tsou wrote:
> Dear TPP developers,
>
> I have a question regarding how iProphet handles
Dear TPP developers,
I have a question regarding how iProphet handles ambiguous I/L IDs from
different search engine. I am using X!Tandem, Comet, and MSGF+ and combine
the results using iProphet, and noticed that the three search engines have
different rules ranking I/L hits.
So how does
