Hello,
May I ask one question related building library with Spectrast?
I am using Windows command to build the library. There is one question:
whether Spectrast will eliminate all the peptide which is less than 6 amino
acid no matter the high peptide phrophet? I am quite interested in some
file by itself.
- Jimmy
On Wed, May 1, 2013 at 1:27 PM, Eileen Yue
y...@ohsu.edumailto:y...@ohsu.edu wrote:
Hello everyone.
I have one error information when I tried to analyze peptide for SILAC data. I
do not know whether this is possibly caused by file's name which includes +
and - . I did
content inside the pep.xml files, consider starting from the beginning
with a re-named mzML file, do the search to generate a pep.xml file and then
run the TPP tools.
- Jimmy
On Fri, May 3, 2013 at 3:49 PM, Eileen Yue
y...@ohsu.edumailto:y...@ohsu.edu wrote:
Hi Jimmy,
thank you for your advice
Hello everyone.
I have one error information when I tried to analyze peptide for SILAC data. I
do not know whether this is possibly caused by file's name which includes +
and - . I did manually change the pep.xml and mzml files's name (which I
deleted + and - ) but I still get error
at just past 2.05GB on Windows.
- Jimmy
On Thu, Oct 20, 2011 at 2:14 PM, Eileen Yue y...@ohsu.edu wrote:
Hi Jimmy:
After I tested one fraction, I run TPP for my 12 fraction together to analyze
the xpress and Asap ratio. They run smoothly and completed after two days.
There is similar problem
the prot.xml file whereas that link for xpress
attempts to grab all related peptide entries from the pep.xml to
display. I don't know ASAPRatio well enough to give you a better
explanation than that.
On Thu, Oct 27, 2011 at 2:21 PM, Eileen Yue y...@ohsu.edu wrote:
Jimmy:
Thank you for your help
, everything is fine.
Do you know how I solve this problem?
Thank you
Eileen
From: spctools-discuss@googlegroups.com [spctools-discuss@googlegroups.com] On
Behalf Of Eileen Yue [y...@ohsu.edu]
Sent: Tuesday, October 18, 2011 3:22 PM
To: spctools
to the filename). But come to think of
it, did you convert it to mzXML or mzML files?
-Joe
On Mon, Oct 17, 2011 at 12:16 PM, Eileen Yue
y...@ohsu.edumailto:y...@ohsu.edu wrote:
Dear Joseph:
Thank you for your kind help!
I followed your advice and copied the executable files on FTP site, which you
put
/dist/XPressPeptideUpdateParser.cgi
The files should go in c:\inetpub\tpp-bin\. Let me know if this fix
does not work for the problem you're experiencing.
- Jimmy
On Tue, Oct 18, 2011 at 10:51 AM, Eileen Yue y...@ohsu.edu wrote:
Hi Joe:
I did convert mzml files. the problem is that the error
Dear all:
I just download the newer version. When I tried to convert my sequest search
results into pepxml, I can not select the files. they showed there are no
files of requested type (tandam) in this directory though I can see my files
listed in the right folder side.
Also when I tried
Is there anyone who know this problem? I tried several times but all of them
failed.
Thank you for your kind help
Eileen
From: spctools-discuss@googlegroups.com [spctools-discuss@googlegroups.com] On
Behalf Of Eileen Yue [y...@ohsu.edu]
Sent: Friday
one of the files.
-Joe
On Mon, Sep 19, 2011 at 10:14 AM, Eileen Yue
y...@ohsu.edumailto:y...@ohsu.edu wrote:
Is there anyone who know this problem? I tried several times but all of them
failed.
Thank you for your kind help
Eileen
From:
spctools
Dear All:
May I check with one problem about converting sequest results to pepxml file?
somehow I met some problem and they showing
'run_in' is not recognized as an internal or external command,
operable program or batch file.
Command FAILED
I do not know why this happen? I also put
Dear All:
I just installed tpp 4.4 in my computer. somehow there is some error
information :
* c:/Inetpub/wwwroot/ISB/data/isk946/ISK946_ER_SCX_1_20110404_VE.pep.xml [
Unreadable! ]
Command 1 [Tue May 17 15:54:06 2011] [ Show / Hide ]
run_in
Dear All:
When I tried to run peptide and protein analysis, the TPP shows the following
error information. Could anyone know what this means?
Thanks
Eileen
command completed in 3 sec
running: C:/Inetpub/tpp-bin/PeptideProphetParser interact.pep.xml
MINPROB=0.85
(SEQUEST)
MS Instrument info:
Dear All:
May I check one qestion about the computer setting for TPP search? Currently, I
am using one PC, which has the duo core and 2G Ram. When I try to analyze the
Velo data (almost 4 G for raw file and 12 G for the dat file) for Asap ratio
and Xpress ratio, it will take very long time.
Dear All:
Several days ago, I post the message to seek some help for analyzing big size
file. Now when I do the peptide and protein analyse, there are the following
error information coming out:
running: C:/Inetpub/tpp-bin/DatabaseParser interact.pep.xml
command completed in 11 sec
Error:
). Will not work doesn't provide enough
information for anyone to make a helpful observation.
Brian
On Mon, Mar 8, 2010 at 3:59 PM, Eileen Yue
y...@ohsu.edumailto:y...@ohsu.edu wrote:
Dear All:
Last time, I send this message to this mail list and want to get some advice. I
still do not solve the problem
] On Behalf Of Eileen Yue
Sent: 10 March 2010 14:28
To: spctools-discuss@googlegroups.com
Subject: RE: [spctools-discuss] how to analyze the big file size date with TPP
Hi Brian:
Thank you for your advice!
In fact, after I load 5 or more fractions, the computer is so slow and I wait
so long
to help me to analyze all the data. The major things that I
need combine all the fraction and get protein ASAP ratio.
Thank you for your kind help
Eileen
-Original Message-
From: spctools-discuss@googlegroups.com
[mailto:spctools-disc...@googlegroups.com] On Behalf Of Eileen Yue
Sent: 04
Dear All:
I tried to use TPP to analyze the SILAC data produced from Velo under Xcaliber
2.1. The sequest results for each fraction is very big and I have total 30
fraction. I tried ONE fraction with TPP and it is fine to convert the raw data
into mzxml and sequest results to pepxml. When I try
I try to use TPP to analyze the SILAC results, which is from Velo (Xcalibar :
2.1). The result files (total 30 fraction files) are really big (14G after
zipped). I tested one fraction with TPP and it can transfer to mzxml and pepxml
after I install Xcalibar 2.1. When I tried to load more such
Dear All:
I try to use TPP to analyze the SILAC results, which is from Velo (Xcalibar :
2.1). The result files (total 30 fraction files) are really big (14G after
zipped). I tested one fraction with TPP and it can transfer to mzxml and pepxml
after I install Xcalibar 2.1. When I tried to load
Dear all:
May I check one question? After I run analysis peptide with TPP, I export to
excel mode. Then I will see all the different column lists all the information
that showed in web but I also noticed that there are some extra information,
such as “adjusted ratio mean”. What does this
AM, Eileen Yue y...@ohsu.edu wrote:
May I check with one question?
I use bioworker to run the database search. I noticed that if I use the
indexed database search, after I load on the TPP to do the protein
probability analysis. TPP will not work.
I can not use indexed database to run
Dear all:
May I check one question? I am doing SILAC analysis with LCQ OR LTQ.
After I load the data to run the peptide analysis in TPP, I select the running
protein probability, asap xpress ratio. I am wondering whether the software
kicks out all the duplicated peptides (the peptide come from
May I check with one question?
I use bioworker to run the database search. I noticed that if I use the indexed
database search, after I load on the TPP to do the protein probability
analysis. TPP will not work.
I can not use indexed database to run the search in order to load on TPP for
ananlysis with indexed
database
That's right, the indexed database format is nonstandard and TPP doesn't
know how to read it. I think, though, that if you provide the nonindexed
version then you can probably have it both ways.
On Fri, Sep 4, 2009 at 11:05 AM, Eileen Yue y...@ohsu.edu wrote
Dear All
When I tried to run the peptide analysis, after I set all the parameters and
start to run, there will be a error showing PeptideProphetParser.exe has
encountered a problem and needs to close. We are sorry for the inconvenience.
I tried to restart the computer but it does not work. I
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