rate is 7 and the total
count of DECOY ids is 9 (out of 5308 PSMs).
You can find the new interact files
here:https://www.dropbox.com/t/s7ZqgkP1f0Yzl0Xn.
Many thanks,
Oded
On Wednesday, 14 April 2021 at 08:34:42 UTC+3 David Shteynberg wrote:
> Hi Oded,
>
> I think the old 5.2.0 might
own%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000=LBdAB3QsH9rUxvNKMwKjOKYDbQXFxma9dREKgS5siWQ%3D=0>
Thanks,
Oded
On Tuesday, 13 April 2021 at 03:38:33 UTC+3 David Shteynberg wrote:
> Dear Oded,
>
> Thanks for this. I ran a quick test and I actually observed a f
And also the search results with the new vs the old version (although I
think they are more or less the same):
https://www.dropbox.com/t/8VyBVdeuoWdk982q
On Tuesday, 13 April 2021 at 00:09:05 UTC+3 Oded wrote:
> Hi David,
> You can find the mzML, Comet parameters and FASTA file here:
&
Hi David,
You can find the mzML, Comet parameters and FASTA file
here:https://www.dropbox.com/t/Yld0ZBWhsuFajeLj
The link is valid for 7 days.
Many thanks,
Oded
On Monday, 12 April 2021 at 23:46:08 UTC+3 David Shteynberg wrote:
> I don't mind taking a crack at it over vacation. Please let
Hi David,
Thank you for the quick reply. We are using TPP v6.0.0-rc14 Noctilucent,
Build 202103031119-8400 (Windows_NT-x86_64).
As for the data let me know when you are back and I will transfer you
either the raw file or the search results.
Enjoy your vacation.
Thanks,
Oded
On Monday, 12 April
.
This seems that this is due to changes in PeptideProphet and are not
related to the search itself that was done with Comet.
Is there any additional parameter that should be included in the new
version in order to restore the missing peptides?
Many thanks,
Oded
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NKOUT=yes=ATAGDTHLGGEDFDNR>
I hope you can advise.
Thanks
Oded
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-Ox and protein N-term acetylation as set as variable
modifications.
When I try to run PTM prophet (following peptide prophet and iprophet runs)
I getting the following error:
EXECUTING: run_in c:/Inetpub/wwwroot/ISB/data/Oded/Enzo/Phospho_June2014;
c:\Inetpub\tpp-bin\PTMProphetParser
STY
Thanks Ulrich.
As always - you got it!
All the best,
Oded
On Feb 3, 7:31 pm, Ulrich auf dem Keller uadkel...@me.com wrote:
Hi Oded,
the workaround is to comment out conditions for LITTLE_ENDIAN in
/extern/ProteoWizard/pwiz/pwiz/utility/misc/endian.hpp:
change to:
// #if (defined(PWIZ_GCC
: error: #error
Unsupported platform: probably need a platform-specific define
above.
make: *** [/Users/OK/Downloads/TPP-4.5.1/trans_proteomic_pipeline/
src/../build/darwin/SHA1.pwiz.o] Error 1
Can someone advice?
Thanks,
Oded
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to overcome it?
Many thanks,
Oded
-- Forwarded message --
From: Jimmy Eng jke...@gmail.com
Date: Dec 21 2010, 8:16 am
Subject: XPRESS discrepancy between PepXML viewer and XPRESS viewer
To: spctools-discuss
Oliver,
I finally had a chance to revert to 4.3.1 on two machines (linux
to that too?
Are there any plans to include the label-free related options
(quantification and visualization) in the GUI.
Many thanks,
Oded
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Hi all,
Is there a way to use fasta.pro files (for X!Tandem search) with the
TPP?
Thanks,
Oded
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Hi all,
I am trying to install the latest TPP code (version 4984) on my Mac
that runs 10.5 using fink.
All seems to go well but a Java related issue in the build of PepC is
causing the following error:
[javac] /Users/oded/tpp4984/src/Quantitation/Pepc/src/
PepcViewer.java:52: cannot find
after exporting ProteinProphet output (while
checking the show peptides option) but currently only the mean ratio
is being exported and not the specific ratio of each peptide within a
protein.
Thanks,
Oded
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Thanks Jimmy - that would be great.
Oded
On Apr 7, 6:24 pm, Jimmy Eng jke...@gmail.com wrote:
Sadly the need for manual inspection isn't going to go away soon but
things will get better with peak picking. I'll look into adding using
median instead of mean as a user option.
On Wed, Apr 7
Hi ,
Is it possible to get this bug fix (thanks again Brian) into windows
installation package?
Thanks,
Oded
On Aug 17, 9:48 pm, Brian Pratt brian.pr...@insilicos.com wrote:
It would be interesting to see the difference between themzXMLfile that
worked and the one that didn't.
X!Tandem has
Thanks Natalie,
On Sep 9, 11:57 pm, Natalie Tasman natalie.tas...@insilicos.com
wrote:
Hello Oded,
Please see the recently released 4.3.1 version of the TPP, which
contains the fix that you mention.
Best wishes,
Natalie
On Sep 9, 2009, at 12:49 PM, Oded wrote:
Hi
of the TPP when
specified.
Good luck,
Oded
On Jun 14, 2:10 am, James Dowell jadow...@hotmail.com wrote:
Hi,
I am trying to set-up the TPP to run an X!Tandem search. I've read
Jimmy Eng's tutorial on using X!Tandem within the TPP. The problem
I'm having is editing the X!Tandem parameters file
(if there
is one)?
Any help would be highly appreciated.
Oded
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and X!tandem and not Sequest (as far as I
remember there were some posts in this list that the 2 searches are
even better) .
BTW - I can't see the 2 screen captures you mentioned in your original
message.
On Apr 23, 7:49 pm, Xin Wei catroy...@gmail.com wrote:
Hi Oded,
Let me see if I understand you
}
This work pretty well for me on the peptide level but I wonder if
there is a way to use this data and get info on the protein level
using the TPP (or else). The best thing would be to get this data
somehow into protein prophet but if there is another way that would be
great.
Thanks for any help.
Oded
help.
Oded
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on RPP v4.2
on PC with winXP.
Thanks,
Oded
On Mar 20, 7:50 pm, Ulrich auf dem Keller ukel...@interchange.ubc.ca
wrote:
Hi Natalie and David,
I am using iProphet to combine results from different search engines
on the same experiment. It works very well and enhances the number of
reliable
are identical.
I hope that might help.
Oded
On Mar 13, 8:34 pm, Dave @ UPENN davejun...@gmail.com wrote:
Hey,
I've never encountered this before but when i try to run xinteract,
peptideprophet hangs during the initializing stats step. i tried
fooling around with the settings with no avail. i
) .
Cheers,
Oded
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spctools
03 11:16:52 2009] [error] [client 127.0.0.1] Premature end of
script headers: plot-msms.cgi, referer:
http://localhost/ISB/data/OK1/June07/interact.pep.shtml
Cheers,
Oded
On Mar 2, 9:43 pm, Brian Pratt brian.pr...@insilicos.com wrote:
Oded,
I'm sure you're right in your diagnosis, and thanks
hard to
fix)
Cheers,
Oded
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such peptides are used in Xpress or ASAPratio analysis? from a
quick check it seems that the peak area is always calculated for the
+1 shift even if the shift is of +2.
Thanks,
Oded
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).
Cheers,
Oded
On Jan 23, 8:37 am, Walter w.blackst...@gmail.com wrote:
Hi,
Useful fixes, but the original question seems unanswered. Is it
correct that only one core and a single thread are utilised? Is this
true for TPP in general? (No criticism implied BTW, just need to plan
the hardware
Thank you Natalie and Luis - following your advice and using yesterday
release things are working fine now.
Cheers,
Oded
On Nov 17, 8:38 pm, Luis Mendoza [EMAIL PROTECTED]
wrote:
Hello,
2) Thank you for reporting the tandem/mzML issue. We'll take a look.
Ah yes, this is a new change (mzML
Hi Natalie,
I checked it once and it seems to work!
I'll keep on testing it and let you know if I found something wrong.
Thanks,
Oded
On Nov 15, 3:55 am, Natalie Tasman [EMAIL PROTECTED]
wrote:
Oded,
I tested your data-- please try again with 4.1.1 and let us know if it's
resolved
this using both mzXL and mzXML and on 2 different
machines.
Hope there is a quick solution.
Best regards,
Oded
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