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
Please note - I've discovered a similar problem (no models html file
generated) in the following thread:
https://groups.google.com/forum/#!searchin/spctools-discuss/interact$20prot%7Csort:date/spctools-discuss/Yrg2yEO4otg/8u0bNKzpAAAJ
Cheers
Pete
On Monday, 11 June 2018 14:58:53 UTC-7,
Hi Luis,
I've got the same problem with my dataset (also a large dataset, combining
multiple experiments). - No models html file is generated.
Please can you tell me if this issue was resolved?
Thanks
Pete
On Monday, 7 May 2018 19:01:28 UTC-7, Luis wrote:
>
> Hi Heeyoun,
>
> Does it seem
Hi Luis,
I suspect that my problem may be due to multiple installations of TPP (from
this post):
https://groups.google.com/forum/#!msg/spctools-discuss/Tq-i-7SVoJE/4XZcq4EGCgAJ;context-place=forum/spctools-discuss
I had originally installed 5.1 in a preferred location, but parts of TPP
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
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
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
