Dear TPP members,
How to calculate the fold change values in LIBRA quantification result?
According to my understanding, the mean value in channel like 115
(treatment group) divided by mean value in channel 114 ( this my control
sample) . If i am wrong, kindly tell me the correct procedure?
1
Dear TPP members,
Is it necessary to include Decoy sequences in search target database to
apply PeptideProphet in TPP? My understanding of PeptideProphet
is probabilistic based approaches, In contrast to
the target-decoy database search approach, appending decoys is not
necessary for deriving t
. 2"
>
> Search start: 06/21/2016, 08:30:56 PM
> - Input file: LTQ_FT.mzXML
>- Load spectra: 5473
> - Search progress: 100%
> - Post analysis: done
> Search end:06/21/2016, 08:31:18 PM
>
>
> On Sat, Jun 18, 2016 at 2:59 AM, Vijay Kumar > wrote:
>
to you.
>
> Similarly, no one repond to my question concerning PTMprophet.
>
> Have you succeeded to run peptideprophet and iprophet?
>
> On Sun, Jun 19, 2016 at 2:47 AM, Vijay Kumar > wrote:
>
>> Hi,
>> Where i will get the complete step wise tutorial for Decoy peptide
Hi,
Where i will get the complete step wise tutorial for Decoy peptide and
protein validation including Mayu procedure for TPP.
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Hi,
When i am running peptideprophat with selection Decoy database option, i
got following error message. Can any one tell me what is the problem in
this analysis? How can i solve the problem?
c:\Inetpub\tpp-bin\xinteract (TPP v4.8.0 PHILAE, Build 201411201551-6764
(mingw-i686))
running: "C:/I
Hi,
When i am running peptideprophat the result shows as
PeptideProphet (TPP v4.8.0 PHILAE, Build 201411201551-6764 (mingw-i686))
AKeller@ISB
read in 0 1+, 17826 2+, 19868 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.
What is the meaning of this? Is it that there is no spectra in 1+, 4+, 5+,
6+ an
Hi,
When i am running pep3d image for my mzXML data , i got following message.
how can i solve this problem? But i am running for mzML data i got pep3d
image.
Messages*[ Show | Hide ]*
- Generating images...
- Empty spectrum (no MS1 data?) in
c:/Inetpub/wwwroot/ISB/data/17052016_NISHA
Hi,
when i am running my mzML data using comet i got load spectra Number is
694.
when i am running the same data in mzXML format using same comet parameters
the load spectra Number is 4508.
Is it possible to get different number of spectra in different format for
same data?
can any one tell wha
Hi Luis,
Thank you for your kind response. If i change minimum intensity value at
Libra condition level, say now default is 20 if change to 10 or what ever
is low is it correct way to increase no of protein with quantification
level?
On Tuesday, June 14, 2016 at 1:42:16 PM UTC-7, Vijay
Hi,
if i select Force the fitting of the mixture model option in
PeptideProphet analysis, what are the caution i have consider? Is it good
option for PeptideProphet when i am getting error message that
WARNING: Mixture model quality test failed for charge (2+).
WARNING: Mixture model quality te
Hi,
I am running Libra for my iTRAQ 4 plex, the commands are successful and i
got result also. How can i read this result and what is meaning -9 in all
four channel?
2 sp|F1NSM7|OC116_CHICK *1.*
coverage: 7.3% LIBRA (0)
114.0: -9.00 ± -9.00
115.0: -9.00 ± -9.00
116.0: -9.00 ± -9.00
117.0:
er has. As email likely won't work for
> such large files, use a service like Dropbox or OneDrive to get me the
> files and I'll investigate.
>
> - Jimmy
>
> On Sun, Jun 12, 2016 at 11:09 AM, Vijay Kumar > wrote:
>
>> Hi,
>> I am running
Hi,
I am running comet database search for my 15 fraction of mzXML data file
from WATERS QTOP. Out of 15 fractions only 5 fractions command are
success, remaining fraction has the following error
*EXECUTING: cd c:/Inetpub/wwwroot/ISB/data& c:\Inetpub\tpp-bin\comet
-Pc:/Inetpub/wwwroot/ISB/dat
Hi,
I am running TANDEM database search for my 15 fractions of mzML file from
WATERS QTOP in TPP. Out of this 15 fractions, only 4 fractions command were
sucessful, remaining fractions show following error
*EXECUTING: cd c:/Inetpub/wwwroot/ISB/data& c:\Inetpub\tpp-bin\tandem
c:/Inetpub/wwwroot
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