hey david,
i uploaded 2 files:
1) the original output file of crux: B08-02057_original_crux.pepXML
2) the pepxml with the latest modifications/adaptations discussed in this
thread: B08-02057_latest_try_to_adapt.pepXML
the original file is an invalid xml. i already reported this to the
crux-maili
Hi Andreas,
Would you mind sharing on of your crux pepXML files? You can post it
to our ftp site:
http://tools.proteomecenter.org/wiki/index.php?title=TPP:Frequently_Asked_Questions#How_do_I_upload_files_to_the_SPC_tools_team.3F
Thanks,
-David
On Wed, Feb 2, 2011 at 1:08 PM, Andreas Quandt wr
Mysterious. If that's really what's going on I'd think you could make
any number of reader tools tip over, have you tried any?
On Wed, Feb 2, 2011 at 1:05 PM, dre wrote:
> The byteorder attribute in my test file is set to "network".
>
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The byteorder attribute in my test file is set to "network".
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hey david,
thanks for answering!
i used xinteract -dDECOY_ -OAdPlIw B08-02057_mod.pepXML to process the file.
as you suggest using a trunk version: can you refer to a specific revision?
cheers,
andreas
On Wed, Feb 2, 2011 at 9:57 PM, David Shteynberg <
dshteynb...@systemsbiology.org> wrote:
> Y
Your best bet is to try the code from trunk SVN. Have you tried it in
NONPARAM mdoe?
-David
On Wed, Feb 2, 2011 at 12:52 PM, Andreas Quandt
wrote:
> hey jimmy and matt,
> i tried what jimmy suggested but are stuck again :-(
> i added the 'missing' scores as jimmy suggested:
>
>
hey jimmy and matt,
i tried what jimmy suggested but are stuck again :-(
i added the 'missing' scores as jimmy suggested:
and get following output:
running: "/cluster/apps/tpp/4.4.1/bin/PeptideProphetParser
'interact.pep.xml' DECOY=DECOY_ ACCMAS
It's probably emitting mzXML 3, which has a byteOrder attribute in the
Peaks element.
On Wed, Feb 2, 2011 at 3:20 AM, dre wrote:
> Hey guys,
>
> No bugs here - I just have a question for the mzXML format experts.
> I've been trying to learn about the format these days and I'm a little
> bit stuck
Hey Jimmy,
I tried the renaming but of course not the adding of the 'missing'
scoring values.
I report back to you guys as soon as I have tested it :-)
Cheers,
Andreas
On Feb 2, 2011, at 5:51 PM, Jimmy Eng wrote:
> Andreas,
>
> I didn't say it was going to be easy! :)
>
> Here's an example S
Hey Matt,
I already tried the substitution of the scoring names but
unfortunately without success...
Cheers,
Andreas
On Feb 2, 2011, at 5:42 PM, Matthew Chambers wrote:
> Did you try renaming the score names? I expect that there is a 1:1
> relationship between the search engine name and the
Hey guys,
No bugs here - I just have a question for the mzXML format experts.
I've been trying to learn about the format these days and I'm a little
bit stuck on the data encoding. The mzXML 2.1 specification states
that data should be encoded from IEEE float to Network binary to Base
64, however
Andreas,
I didn't say it was going to be easy! :)
Here's an example Sequest pep.xml file:
http://proteomicsresource.washington.edu/dist/sequest.pep.xml
As Matt suggested, the search_score names will need to change
("xcorr_score" to "xcorr" and "delta_cn" to "deltacn"). Additionally,
you'll prob
Did you try renaming the score names? I expect that there is a 1:1 relationship between the search
engine name and the score names (correct me if I'm wrong TPP folks). If you need a program to do the
"replace all" you can try Notepad++ or Gvim.
-Matt
On 2/2/2011 10:22 AM, Andreas Quandt wrote
sure :-)
originally the spectrum query match looks like
(to the original sequest, the difference is also that the scores are named:
xcorr and deltacn...)
--andreas
On Wed, Feb 2, 2011 at 5:04
Can you paste a few of the spectrum_query elements? It seems like you got it to process properly as
SEQUEST, so there's something wrong further down.
-Matt
On 2/2/2011 9:56 AM, Andreas Quandt wrote:
hey matt,
thanks for picking this up.
i posted the original first lines of the crux file not
hey matt,
thanks for picking this up.
i posted the original first lines of the crux file not all the tries to
modify them ;-)
after fixing the xml structure manually (the originally produced xml file is
marked as not well-formed by xmllint), i tried several variations. one of
them is posted below:
How did it process it as Sequest if the search_engine attribute still says
"Crux"?
-Matt
On 2/2/2011 5:30 AM, Andreas Quandt wrote:
hey jimmy,
thanks for the reply!
i tried to follow your advice wtih modifying the pepxml produced by crux.
however it seems i am not pulling the right strings.
hey jimmy,
thanks for the reply!
i tried to follow your advice wtih modifying the pepxml produced by crux.
however it seems i am not pulling the right strings.
when having a crux header like this:
i tried various modifications of the msms_run_summary and the search_summary
tags but i
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