me know.
>
> Since you're using linux, build XPressPeptideParser from either the
> trunk or branch4-5 code.
>
> On Thu, Oct 20, 2011 at 2:04 PM, Ping wrote:
> > Hi,
>
> > I installed tpp 4.5 on a Ubuntu 10.04 system. While I run
> > XPressPeptideParser o
something with mzXML file.
Can anyone help?
Thanks,
Ping
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spctoo
e_t temp= fread(buffer,1,200,f);
saxmzxmlhandler.cpp:size_t temp= fread(buffer,1,200,f);
Thanks,
Ping
On Oct 4, 11:37 am, Ping wrote:
> No I tired to on ubuntu 10.4 using installer_linux
>
> The error message I got is after I run
>
> sh ./install-prerequisites-ubuntu
No I tired to on ubuntu 10.4 using installer_linux
The error message I got is after I run
sh ./install-prerequisites-ubuntu-9_04.sh
cd ../src/
make
Thanks,
Ping
On Oct 3, 4:34 pm, Joseph Slagel
wrote:
> Are you trying to install using the window's installer, or build it? and if
/mzParser/mzParser.h:3617: error: ‘uint32_t’ has not been
declared
Parsers/mzParser/mzParser.h:3618: error: ‘uint64_t’ does not name a
type
Did I do something wrong?
Thanks,
Ping
On Sep 21, 4:50 pm, Joseph Slagel
wrote:
> Announcing the availability of Trans-Proteomic Pipeline (TPP) "Rapt
le). Example
> > modifications include a +16 variable mod on methionine and a static
> > mod of +57 on cysteines:
> > http://proteomicsresource.washington.edu/sequest_params.php
>
> > What we really need is someone to contribute a .msf to pep.xml converter!
>
> > On Thu, Ma
cysteines:
> http://proteomicsresource.washington.edu/sequest_params.php
>
> What we really need is someone to contribute a .msf to pep.xml converter!
>
>
>
> On Thu, Mar 4, 2010 at 3:49 PM, Ping wrote:
> > Thanks Jimmy!
>
> > Is there any sequest.params sample wi
Thanks Jimmy!
Is there any sequest.params sample with modifications I can get?
Thanks again!
Ping
On Mar 3, 5:16 pm, Jimmy Eng wrote:
> unless there's a way to convert .msf to pep.xml, and I'm not aware of
> any tool that does this, you'll have to go the .out route.
Hi All,
The output of the Proteome Discover is *.msf. Is there an easy way to
compute peptide prophet from it? Or I have to run sequest.exe to get
*.out to do so?
Thanks!
Ping
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Hi All,
Has anyone build OMSSA under Ubuntu 64 bit? I got it successfully
complied along with NCBI tool kit, but it got very slow now. I noticed
that it only use one processor instead of original 8 processors to
run the omssacl.
Does anyone have any suggestion on this?
Thanks!
Ping
That is where I got the NAN error at the first point.
Thanks,
Ping
On Jul 14, 8:46 am, GATTACA wrote:
> Ping,
>
> Could you post what changes you made to the
> NonParametricDistribution.cxx to fix the NAN error?
>
> Thanks.
>
> On Jul 9, 1:21 pm, Ping wrote:
&
Hi,
I got a list of the search results which used different search
parameters, I already run InteractParser and PeptideProphetParser on
each of them. Is there an easy way to merge individual pep.xml into
one pep.xml file and with the hits ranked by peptide prophet?
Thanks,
Ping
suggested, I do
not need to replace the value in the "protein" with the first word
from the "protein_descr" in each search_hit entry.
Thanks again,
Ping
On Jul 6, 1:55 pm, Jimmy Eng wrote:
> Has anyone been able to feed OMSSA native pepXML output (using -op
> option)
!
Is there anything else I need to fix?
Thanks!
Ping
Here is the example of the result after I replace protein/
protein_descr
for not decoy string, it looks like this:
For decoy string, it looks like this:
On Jul 2, 4:44 pm, Jimmy Eng wrote:
> Ping,
>
> I just downloa
Jimmy,
As you suggested, I replace the value in the "protein" with the first
word from
the "protein_descr" in each search_hit entry:
for not decoy string, it looks like this:
For decoy string, it looks like this:
Is there anything else I need to fix?
Thanks!
.cpp", line 228: Error: NCBI-BlastDL::Blast-def-line.title
Ping
On Jul 3, 3:46 am, Jake W wrote:
> One solution to this is to use the indexing option ("-o T") in
> formatdb when formatting your BLAST database for OMSSA searching. In
> my experience, that will result
alert the
developer !!!
I will try Jimmy's suggestion and see how it goes.
Thanks again!
Ping
On Jul 2, 7:15 pm, David Shteynberg
wrote:
> If you are running the tpp on the commandline you can correct this
> problem in theomssaoutput by running the steps of xinteract
> separatel
Jimmy,
Thanks a lot for your explanation. I am going to write a script to fix
the pep.xml file and see how it goes.
Ping
On Jul 2, 4:44 pm, Jimmy Eng wrote:
> Ping,
>
> I just downloadedOMSSA2.1.4 and tried the direct pep.xml export
> myself. I do see a problem with the resul
Does any one have suggestion on this problem? I used the omssacl -op
option to generate the pepxml result. Will this cause problems?
Thanks,
Ping Yan
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Is this something else and suppose to be a new post?
YP
On Jun 30, 11:08 am, "Zhi Sun" wrote:
> Hi all,
>
> I just checked in two programs, and did not put the log message.
>
> I will give a short description here:
>
> createChargeFile.pl: this program reads the ms2 file generated by CPM
> (cha
t is still not working. InteractParse went through, but
PeptideProphetParser got stuck by a segmentation fault.
Any help would be greatly appreciated!
Many Thanks,
Ping
* output for interactParser and PeptideProphetParser
InteractParser 'interact.pep.xml' 'omssa.pep.xml' -
Luis,
Thanks a lot!
I just realize that the xml file from TPP output is already run
through PeptideProphet with 0.05 cutoff.
I will try to rerun the xtandem along to see how it works.
Best,
Ping
On Apr 16, 11:52 am, Luis Mendoza wrote:
> Hello Ping,
> Yes, please make sure you run xin
searched under X!tandem. The result
I used is from TPP.
Thanks again!
Ping
On Apr 15, 3:42 pm, Luis Mendoza wrote:
> Hi Ping,
> By "the same results", do you mean that all of the program output is
> identical? (e.g. the number of spectra used, etc) Or just that you also get
>
search for the same topic in the
group. Someone said it might because of the mzXML files?
Thanks again!
Ping
On Apr 15, 11:44 am, Luis Mendoza wrote:
> Hello Ping,
> Qualscore uses a pepXML file with *all* PeptideProphet probabilities (i.e.
> P>=0.0). As such, you will first need to
searched the post in the group, and used -p0 option, but still I got
the same results. Does that mean my original mzXML has too little low
quality spectral data?
Thanks again,
Ping
On Apr 15, 11:44 am, Luis Mendoza wrote:
> Hello Ping,
> Qualscore uses a pepXML file with *all* PeptideP
forgive me if the question is
too simple.
Thanks!
Ping
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