ys).
>
> Henry
>
> On Friday, July 20, 2018 at 5:10:29 AM UTC+8, Chih-Chiang Tsou wrote:
>>
>> Hi TPP developers
>>
>> I used SpectraST to generate decoy spectra and I noticed there are decoy
>> spectra generated based on shuffled sequences with AAs add
Hi TPP developers
I used SpectraST to generate decoy spectra and I noticed there are decoy
spectra generated based on shuffled sequences with AAs added randomly. Is
there option to disable it?
Below is the message I got from spectrast:
DECOY: Shuffle DFGLTSLALV to DSTLLGAFLVMGV. (3 AAs added
> On Tue, Jun 12, 2018 at 9:06 AM, Chih-Chiang Tsou <
> chihchiang.t...@gmail.com> wrote:
>
>> 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
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
al possibilities. First of all, which
> version of the TPP are you on and what options are you using for
> xinteract? It is possible that the repeating spectrum names are confusing
> PeptideProphet.
>
> Thanks,
> -David
>
> On Tue, Apr 4, 2017 at 11:39 AM, Chih-Chiang Tsou <
Hi
Is there any option in xinteract to tell PeptideProphet take topN hits for
each spectrum for probability calculation?
Thanks,
Chih-Chiang
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from the unmodified peptides. That said, learning
algorithms such as this perform best when trained with enough data.
If modified peptides are only a small part of the set they may not be
very well characterized by the algorithm.
-David
On Sat, Dec 6, 2014 at 12:33 PM, Chih-Chiang Tsou
on peptide amino acid positional
information and other peptide properties. They are different learning
algorithms.
-David
On Fri, Dec 5, 2014 at 9:36 AM, Chih-Chiang Tsou
chihchi...@gmail.com javascript: wrote:
Hi David,
I am trying to use rtcalc to train a prediction model directly
Hi David,
I am trying to use rtcalc to train a prediction model directly from PepXML.
Is the option PEPXML for that? it didn't work for me.
Another question is what's the difference between coefficient file and ANN
model file?
Thanks,
Chih-Chiang
On Tuesday, April 23, 2013 12:29:18 PM UTC-4,
