If you suspect the problem is with the converter (msconvert.exe), try
running that outside of TPP and see if you get any interesting error
messages.
Brian Pratt
On Fri, Sep 27, 2013 at 12:56 AM, Konstantinos Vougas kvou...@gmail.comwrote:
Hello,
I have just completed a fresh installation
Not sure how helpful an answer this is, but (as you perhaps already know)
there are several parallelized versions of X!Tandem that do that for you.
Brian
On Tue, Jan 8, 2013 at 1:59 AM, Gautam Saxena gsaxena...@gmail.com wrote:
FYI: I meant to write MB wherever I wrote GB.
On Tuesday, 8
Just a note to say that Matt is known to be away for the holidays, so this
will probably sit for a little while.
- Brian
On Wed, Dec 19, 2012 at 7:11 AM, Dmitrii Tchekhovskoi
dmitrii...@gmail.comwrote:
I guess, only Thermo may know exactly how to convert NCD into eV.
I am not sure if the
Check out http://proteowizard.sourceforge.net/ - that's where the
msconvert utility is from.
On Sun, Nov 4, 2012 at 7:21 PM, Sam Islander sad...@gmail.com wrote:
I am having trouble compiling TPP in ubuntu 12.10. I think it's related to
boost libs. (version 1.49 is installed by default). I
Quite a lot of performance work was done in pwiz in late 2011 - do you
know what version of pwiz is in use?
Brian Pratt
On Thu, Aug 30, 2012 at 2:16 AM, Thomas Dybdal Pedersen
thomas...@gmail.com wrote:
Hi
I've recently begun to investigate whether it was time to change our
pipeline from
UTC+2, Brian Pratt wrote:
Quite a lot of performance work was done in pwiz in late 2011 - do you
know what version of pwiz is in use?
Brian Pratt
On Thu, Aug 30, 2012 at 2:16 AM, Thomas Dybdal Pedersen
thom...@gmail.com wrote:
Hi
I've recently begun to investigate whether it was time
The best thing would be to just use your new reader code to extend
msconvert so that it *does* read your file. Then you can output to
anything msconvert already handles.
- Brian Pratt
On Wed, Aug 8, 2012 at 8:40 AM, wlstraube stra...@imp.ac.at wrote:
Hello TPP-Team,
I would like to compile
For simplicity, you would probably want to go with the hacking up the
old readw code. But if you have any plans for sharing your work or
using it very far into the future then you're better off with
ProteoWizard and msconvert since that gets maintained and offers more
output formats.
Brian
On
The index is technically optional, you should be able to just skip it
in your output.
(technically and should, as some parsers are brittle and will fail
without it - good luck!)
On Thu, Jun 14, 2012 at 12:38 PM, Ben Temperton btemper...@gmail.com wrote:
Hi Jimmy,
I have updated the scan
That's the simplest way, yes. Although it may have some other pointy
edges on it.
On Fri, Mar 18, 2011 at 5:52 AM, GATTACA dfer...@umich.edu wrote:
So I should try to compile the SVN version?
On Mar 17, 1:07 pm, Brian Pratt brian.pr...@insilicos.com wrote:
Looks like I dealt
Looks like I dealt with that in trunk, back in December. The commit
message was C++ standard (or at least, older, portable revs of the
standard) doesn't allow a ctor to call another variant of itself. But
we can use default parameter values instead to achieve the same
effect..
On Thu, Mar 17,
A well constructed mzXML file would normally be somewhat smaller than
its mzML equivalent - make sure you've got peaklist compression turned
on (IIRC the msconvert default is no compression, which seems like a
Bad Thing to me but there you have it).
On Wed, Mar 2, 2011 at 10:37 PM, ben
, Brian Pratt brian.pr...@insilicos.com
wrote:
That single quote is certainly incorrect. I have fixed that, not sure
if it also corrects your other issues but you should try again with
r5304.
Brian
On Sat, Feb 5, 2011 at 10:03 AM, Andreas Quandt
quandt.andr...@gmail.com wrote:
dear list
That single quote is certainly incorrect. I have fixed that, not sure
if it also corrects your other issues but you should try again with
r5304.
Brian
On Sat, Feb 5, 2011 at 10:03 AM, Andreas Quandt
quandt.andr...@gmail.com wrote:
dear list,
i tried to comile the r5303 from the trunk
No data compression on the peak list?
Try running the file through mscovert, it does not use the RAMP parser
and should give a good sanity check on the mzXML file in question.
Instead of guessing at what's reasonable, I'd advise determining what
the actual value is (again, msconvert could help
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 shee...@gmail.com 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
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 shee...@gmail.com wrote:
The byteorder attribute in my test file is set to network.
--
You received this message because you are
It doesn't change the data, it just performs lossless zlib data
compression on it. I'm not really sure why that isn't the default
behavior.
On Thu, Jan 27, 2011 at 11:40 PM, furukie efur...@etc.a-star.edu.sg wrote:
Hi,
May I know what the option Compress peak lists for smaller output
file
The output from the xinteract command of the analysis stage will
tell you more about your problem than the Apache logs will. The
pepXMLViewer error is probably just a result of some previous failure.
Brian
On Thu, Jan 13, 2011 at 10:03 PM, Furuki Eiko efur...@etc.a-star.edu.sg wrote:
Hi,
don't know what to grab.
Thanks
Damian
On Dec 10, 12:55 pm, Brian Pratt brian.pr...@insilicos.com wrote:
Are you using the TPP build system, and its copy of ProteoWizard, or
are you using the official ProteoWizard build system? If it's the
latter you might be better asking on the proteowizard
TITLE=Foo.5986.5986.4
RTINSECONDS=123.4
PEPMASS=748.617 946661.3125
CHARGE=4
259.9697876 24.20503426
261.1176758 4.82276392
...
END IONS
-Matt
On 12/13/2010 1:08 PM, Brian Pratt wrote:
The code does appear to be looking for and recording the value of
CHARGE= - but that gets lost
Are you using the TPP build system, and its copy of ProteoWizard, or
are you using the official ProteoWizard build system? If it's the
latter you might be better asking on the proteowizard support list.
Brian
On Fri, Dec 10, 2010 at 6:57 AM, GATTACA dfer...@umich.edu wrote:
Hello.
I'm trying
. I have succeed to download other files from
other website, showing there is no filter preventing downloading. I am
in the University in China, maybe internet is not very good. So could
you tell me another website where I can download the file?
2010/11/23 Brian Pratt brian.pr...@insilicos.com
to
download tutorial data from the website
(http://www.insilicos.com/data/tutorial.exe) to proceed.
On Mon, Nov 22, 2010 at 3:34 AM, Brian Pratt brian.pr...@insilicos.com
wrote:
You shouldn't need anything from the Insilicos website - are you using
the tutorial at
http://tools.proteomecenter.org
You shouldn't need anything from the Insilicos website - are you using
the tutorial at
http://tools.proteomecenter.org/wiki/index.php?title=TPP_Tutorial ?
On Sun, Nov 21, 2010 at 3:40 AM, 钟传奇 andy...@gmail.com wrote:
Hi, everyone. I am fresh to TPP, and want to learn it. I have read
Tans
I expect you need to tweak the Apache config to tell it that it's OK
for the webserver to access that directory.
On Thu, Nov 4, 2010 at 7:59 AM, Cristian cristian.r...@gmail.com wrote:
Dear All,
We have problems seeing files in Petunia (Windows) under working data
directory of TPP installed
Hi James,
Can I have a bit more detail? Click on what, exactly, and in what
context? Where does the text appear? Can you provide the entire
text?
Thanks,
Brian
On Mon, Nov 1, 2010 at 5:50 PM, James Broadbent
james.broadb...@gmail.com wrote:
Hi Everyone,
I'm having a bit of trouble with
it does not. If the readme said that one must build with MinGW
first, I would have been saved many many many hours. Perhaps someone
in the future will have the same need.
And thanks for sticking with me Brian, I will give it a go with MinGW!
On Oct 14, 2:09 pm, Brian Pratt brian.pr
jeffrey.a.mil...@gmail.com wrote:
Hi Brian
Building is no longer essential for me, but I gave it a try anyways.
the fann libraries are sorted out, but the gsl project is a mess of
missing/moved header files. Does trunk build for anyone right now?
On Oct 12, 10:36 am, Brian Pratt brian.pr
of
missing/moved header files. Does trunk build for anyone right now?
On Oct 12, 10:36 am, Brian Pratt brian.pr...@insilicos.com wrote:
Try building from trunk.
That fann stuff came in to the build fairly recently and was probably
pushed into the branch without the accompanying
You'll need to get the entire source tree from
/sashimi/trunk/trans_proteomic_pipeline/ down, them cd to
/sashimi/trunk/trans_proteomic_pipeline/src and make _Mascot2XML.
On Thu, Jul 1, 2010 at 9:58 AM, Ronald W. Finnegan r...@mail.nih.gov wrote:
I have downloaded the MascotConverter.cxx source
windows server?
On Jul 1, 1:42 pm, Brian Pratt brian.pr...@insilicos.com wrote:
You'll need to get the entire source tree from
/sashimi/trunk/trans_proteomic_pipeline/ down, them cd to
/sashimi/trunk/trans_proteomic_pipeline/src and make _Mascot2XML.
On Thu, Jul 1, 2010 at 9:58 AM, Ronald W
: Operation not
permitted
END OUTPUT
RETURN CODE:256
## End Command Execution ##
# All finished at Mon Jun 28 16:24:39 2010
# END COMMAND BLOCK
Any suggestion for fixing this?
Thanks in advance
Jing
On Thu, Jun 24, 2010 at 8:06 AM, Brian Pratt brian.pr
-zero exit code: 11
QUIT - the job is incomplete
[r...@apcf-hn3 2010-06-23]#
On Thu, Jun 24, 2010 at 1:39 AM, Brian Pratt
brian.pr...@insilicos.comwrote:
If you're running this using xinteract, you can debug a little by
adding -t! to the xinteract commandline on the release version, and -t
If you're running this using xinteract, you can debug a little by adding
-t! to the xinteract commandline on the release version, and -t# to the
commandline for the development version. -t! (note the exclamation point)
causes a series of test files to be generated (they're just copies of the
I don't see it there...
On Fri, Jun 18, 2010 at 5:57 PM, Jing Wang fayfay9...@gmail.com wrote:
Hi Brian,
Thanks!
I have uploaded my mascot search file (F030337.dat).
Fay
On Fri, Jun 18, 2010 at 2:52 PM, Brian Pratt brian.pr...@insilicos.comwrote:
Hard to say what's going on. Perhaps
Hard to say what's going on. Perhaps you could upload your new mascot
result file to the files area at
http://groups.google.com/group/spctools-discuss?hl=en. and someone can have
a look.
Brian
On Fri, Jun 18, 2010 at 11:09 AM, Fay Wang fayfay9...@gmail.com wrote:
Hi all,
I posted my
Sure, that's not unusual. Have a look at the makefile to see the individual
targets.
Building on Solaris 10 *is* a bit unusual, though, you may hit some bumps.
On Thu, Jun 17, 2010 at 4:17 AM, sasircm duha...@ircm.qc.ca wrote:
Hello
I would like to intergrate some of TPP programs in a in
= /tpp/cgi-bin/check_env.pl
GATEWAY_INTERFACE = CGI/1.1
SERVER_ADDR = 130.232.69.141
DOCUMENT_ROOT = /usr/local/tpp/html/
WEBSERVER_TMP = /usr/local/tpp/html/tmp
HTTP_HOST = host
On May 21, 3:15 am, Brian Pratt brian.pr...@insilicos.com wrote:
PATH is of interest as well. Or you could just
Hi Oded,
You'll need Java 1.6 - turns out javax.swing.table.TableRowSorter
isn't in 1.5. Can you readily upgrade that?
Brian
On Sun, May 23, 2010 at 3:48 AM, Oded oded.kleif...@gmail.com wrote:
Hi all,
I am trying to install the latest TPP code (version 4984) on my Mac
that runs 10.5 using
I don't see anything on my FTP server, possibly you uploaded to ISB.
But the thing to do is to post it to the files area for
spctools-discuss, as previously suggested:
http://groups.google.com/group/spctools-discuss/files?hl=en
That's your best shot at getting community support, since much of the
at Thu May 20 17:32:43 2010
# END COMMAND BLOCK
Can anyone help?
On Wed, May 19, 2010 at 7:47 PM, Brian Pratt brian.pr...@insilicos.com
wrote:
Yes, those scripts work flawlessly against the (now somewhat old) EC2
base images mentioned in their comments. But I imagine they need
tweaking
also, probably best to start a new thread - this hasn't got much to do
with Installing X! Tandem Under Linux
- Brian
On Thu, May 20, 2010 at 1:28 PM, Brian Pratt brian.pr...@insilicos.com wrote:
Can you post the various files to the spctools-discuss files area?
Sounds like the kind of thing
Yes, those scripts work flawlessly against the (now somewhat old) EC2
base images mentioned in their comments. But I imagine they need
tweaking when used with something newer - linux ecosystems can be
pretty brittle, as you know.
Brian
On Wed, May 19, 2010 at 8:21 AM, EricTan
Have you had a look at the trans_proteomic_pipeline\installer_linux
directory in the source code tree? Those are the configuration
scripts we use on EC2, and for local continuous integration tests.
Brian
On Tue, May 18, 2010 at 2:40 AM, EricTan mefloqu...@gmail.com wrote:
Thanks for the
that I don't feel I can support running TPP
in a Linux environment.
On Mar 23, 6:23 pm, Brian Pratt brian.pr...@insilicos.com wrote:
Start with the tpp_hostname: command not found message. The solution is a
combination of setting the PATH for the webserver user, and customizing your
why is it that the TPP comes with a version of X! Tandem that's about three
years older than the current version?
The TPP version is a fork of X!Tandem that allows pluggable scoring
(that feature is courtesy of LabKey Software) and full mzML and
mzXML.gz read capability (via ProteoWizard
unable to read pepxml file: error parsing pepxml file: XML parsing
error: not well-formed (invalid token), at xml file line 11, column 62
It might be interesting to run it through an XML validator, both before and
after your manipulations, to see if it's actually ill-formed.
Brian
On Thu, May
Not sure how that would work, as pepXML doesn't contain peak lists.
On Tue, May 11, 2010 at 9:09 AM, Jesse J firstblackphan...@gmail.comwrote:
Is there a program that will convert a pepXML file to an mgf file?
--
You received this message because you are subscribed to the Google Groups
Have you had a look at the ReAdW source code?
http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/src/mzXML/converters/ReAdW/
Worth noting, too, that this is being let go in favor of msconvert from the
ProteoWizard project, which is more actively maintained than
What Brendan is suggesting is adding something like this to the k_score
class:
/* Thu, Apr 22, 2010 at 9:26 AM on spctools-discuss, Brendan M said:
I took a quick look at the code, and this function appears to be
related to new handling for phosphorylation. It looked to me like you
could just
The defect is really somewhere upstream - whatever created the pepxml files
that went into xinteract should have escaped those characters.
On Wed, Apr 14, 2010 at 11:25 PM, Simon Michnowicz
simon.michnow...@gmail.com wrote:
Dear Group,
I am running a Peptide Prophet search but xinteract
Actually you decode the base64 to binary data, then decompress compressedLen
bytes of that data to get the binary peaks info you're already used to
dealing with. For an example have a look at
*
http://sashimi.sourceforge.net/trunk/jrap/sax2/src/org/systemsbiology/jrap/SAX2ScanHandler.java
*
Not
My guess would be that the parser is trying to fail gracefully on an out of
memory condition - it forgets part of the stream then is confused when it
hits an unmatched closing tag.
But that's just a guess. Could also be about crossing the dread 2GB file
size threshold.
It's almost certainly
only
a very small fraction of that.
Looked again and the file is *just* over the 2GB boundary, looks like
you're right, which has pointed me to the index file, which shows the
integer offset values have overflowed.
Many Thanks,
DT
On 31 Mar, 17:08, Brian Pratt brian.pr...@insilicos.com
, and long int would give 4GB
on 32-bit or much more on 64-bit systems.
DT
On 31/03/2010 18:36, Brian Pratt wrote:
Do you know how pepXMLViewer.cgi was built? It's meant to support large
files...
On Wed, Mar 31, 2010 at 9:54 AM, dctrud dct...@ccmp.ox.ac.uk wrote:
Hi Brian,
I
tomorrow at where
the
index is created, and what integer types are being used. I suppose an
unsigned int can be used then that'd be good for up to 4GB, and long int
would give 4GB on 32-bit or much more on 64-bit systems.
DT
On 31/03/2010 18:36, Brian Pratt wrote:
Do you know how
Start with the tpp_hostname: command not found message. The solution is a
combination of setting the PATH for the webserver user, and customizing your
tpp_gui_config.pl file to tell the GUI where you installed the various
executables.
Good luck,
Brian
On Tue, Mar 23, 2010 at 6:20 AM, Eliza
Does the file pass general XML validation? That is, did you possibly damage
it structurally?
It's hard to discuss these things without looking at the actual file, can
you upload to the group's files area?
Brian
On Tue, Mar 23, 2010 at 1:20 PM, Andreas Quandt quandt.andr...@gmail.comwrote:
All sound conjectures, but hard to say without laying eyes on the data. Can
you zip one up and post to the group's files area?
On Thu, Mar 18, 2010 at 7:04 AM, GATTACA dfer...@umich.edu wrote:
Hello
We have about 30 mzXML files we have analyzed using X!Tandem/TPP
without any problems.
' file
page, and then reply with a post containing the filename:
http://groups.google.com/group/spctools-discuss/files
On 3/9/10 2:01 PM, Brian Pratt wrote:
I had a look at the three mzXML files you uploaded to Insilicos -
they're quite large (about 1GB each) and it just takes X!Tandem
output.
But if I try run_in c:\; dir, I get:
command dir failed: Unknown error.
Could it be I previously had installed Perl 5.10? I uninstalled it
and then installed Perl 5.8.9 followed by tpp 4.3.1.
Lik Wee
On Wed, Mar 10, 2010 at 1:34 PM, Brian Pratt
brian.pr
Offline.
2. Click the Favorites Center button , click History, and then click
the page you want to view.
*From:* spctools-discuss@googlegroups.com [mailto:
spctools-disc...@googlegroups.com] *On Behalf Of *Brian Pratt
*Sent:* 08 March 2010 16:16
*To:* spctools-discuss@googlegroups.com
Did you have a working TPP installation before?
On Wed, Mar 10, 2010 at 3:54 PM, Lik Wee Lee l...@systemsbiology.orgwrote:
Hi Brian,
On Wed, Mar 10, 2010 at 3:34 PM, Brian Pratt
brian.pr...@insilicos.comwrote:
I think the fact that run_in doesn't work indicates some kind of system
level
and it complained about missing perl so I
downloaded 5.10 and installed it successfully.
But when I ran into problems, I thought it might be due to the perl
version, so I uninstall Perl 5.10.1 and TPP and then reinstall Perl 5.8.9
and TPP.
Lik Wee
On Wed, Mar 10, 2010 at 4:08 PM, Brian Pratt
Hi Eileen,
Perhaps you could start by posting the output from a failed TPP run (just
copy and paste from the TPP GUI). 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.edu wrote:
Dear All:
or directory
Command:PASV
Response: 550 /pub/Hannes_20100301/20091125_AD_Boiani_oocyte_03.raw:
No such file or directory
Error: Critical file transfer error
.
Kind regards,
Hannes
On 26 Feb., 19:18, Brian Pratt brian.pr...@insilicos.com wrote:
Strange indeed. If you
more times now and to me it looks like as if XTandem database
searches are currently only possible in tranches of two. Strange,
isn´it?
Hannes
2010/2/24 Brian Pratt brian.pr...@insilicos.com:
You'll want to narrow it down to identify the problem - for example,
what
happens when you
Looking at the code I can see where this would easily become diskbound for
large data sets - it reads and rereads the same pepXML files repeatedly, but
the effect is probably masked by disk cacheing up to a certain point.
Somebody would need to write some logic for cacheing the file contents to
, but the continued
rpeated slows things down.
R.E. solutions for this, is Boost code welcomed in the main TPP tools? I
think I can re-write using a single pass parse of the .pep.xml into a
Boost.MultiIndex hash of structs/classes containing the required peptide
info.
DT
Brian Pratt wrote
FWIW, the -T option actually does get a mention in the usage statement,
-Tnum where num is a float specifying maximum MH+ scan,
default=4200.0 Da
although it refers to maximum scan instead of maxmum mass, which may
have caused your eye to trip over it. I'll fix that. Thanks for the
I checked in that change on Nov 17.
Brian
On Tue, Nov 24, 2009 at 1:25 PM, Bill Nelson nelson...@gmail.com wrote:
So, is that an error in the code or is my compiler special, that is,
do I change my local copy or has the trunk been updated?
Thanks,
Bill
On Nov 17, 5:14 pm, Brian Pratt
Hi Mike,
I'll have a go at it. It might be easiest if you just emailed me your
modified code directly.
Brian Pratt
On Tue, Nov 17, 2009 at 4:20 PM, Mike Coleman tutu...@gmail.com wrote:
It doesn't look like this patch ever made it into the SVN tree. Could
someone look at adding it? I
might
not see that coming.
Perhaps you could furnish an example of the msconvert output that's giving
you trouble? Eyeballing the code only gets one so far, it's ideal to see it
actually running in the debugger.
Brian Pratt
On Tue, Nov 17, 2009 at 6:33 AM, Dave Trudgian dct...@ccmp.ox.ac.uk wrote
- Brian Pratt
On Tue, Nov 17, 2009 at 6:08 AM, Loïc JOFFRE loic.jof...@gmail.com wrote:
Hello everyone,
I have .omx result files (from OMSSA browser 2.1.1) and I would like
to use the PeptideProphet (TPP v4.3.1).
However, the PeptideProphet only accepts .pepxml files, how could I do
to run
be a little OCD.
Thanks,
Bill
On Nov 17, 2:42 pm, Brian Pratt brian.pr...@insilicos.com wrote:
Glad it's coming along.
There is some weirdness here, though - my copy of out2xml.cxx doesn't
have a
comparison operator at line 752, and it's current with SVN.
Brian
On Tue, Nov
if, at least, the README file had
been updated when the build procedure was changed.
Thanks,
Bill
On Nov 9, 11:59 am, Brian Pratt brian.pr...@insilicos.com wrote:
Can you please guide me to the correct win_lib folder for the trunk or
is it no longer needed?
No longer needed. Instead, things
to
troubleshoot the makefile?
Thanks,
Bill
On Nov 16, 1:34 pm, Brian Pratt brian.pr...@insilicos.com wrote:
Bill,
Agreed, it's bad when the docs get stale. I'll update that windows
readme.
As to the IDE, I'm with you but the bulk of the TPP developers are linux
folk.
Brian
Best approach is to check the logs, and google on what you find there.
On Thu, Nov 12, 2009 at 9:23 PM, Sugu nsug...@gmail.com wrote:
Hi,
I have using ubuntu 9.04 linux, Yesterday I installed PHP and Apache.
Both are working fine, can able to execute those commands.
But today after
Granted, this is a defect - but that's still an unfortunate choice of
characters. Even with the correction I can imagine this tripping up other
software downstream since the properly escaped XML would no longer match the
FASTA on a literal basis. I don't suppose your users could be induced to
are
in the FASTA.
http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+657mP1a3t7q+-e+[IPI:%27IPI00465120.3%27]+-qnum+1+-enum+1
Cheers,
DT
On Nov 11, 7:52 pm, Brian Pratt brian.pr...@insilicos.com wrote:
Yes, one would want to escape everything properly - happily there's a
library call
the msconvert to convert some QQQ
wiff files to mzML format. Are we talking about ABI WIFF or Thermo RAW?
-Matt
Brian Pratt wrote:
You probably mean mzXML rather than mzML?
On Fri, Oct 2, 2009 at 3:55 PM, Zhi Sun z...@systemsbiology.org
mailto:z...@systemsbiology.org wrote
:* spctools-discuss@googlegroups.com [mailto:
spctools-disc...@googlegroups.com] *On Behalf Of *Brian Pratt
*Sent:* Monday, October 05, 2009 9:20 AM
*To:* spctools-discuss@googlegroups.com
*Subject:* [spctools-discuss] Re: msconvert generated mzML file
I don't think Readw ever made mzML files did
in SeeMS, and it is profile mode data.
Zhi, is the mzML on peptideAtlas the result after you added the
peakPicking filter?
-Matt
Brian Pratt wrote:
FWIW those mzML files don't load in InsilicosViewer, which uses the
same pwiz libs as tandem for reading. I'm investigating. The mzXML
samples, but only one sample has spectra.
-Matt
Brian Pratt wrote:
Matt,
FWIW that's actually a 78MB file when extracted from the gzipped
tarball (95MB in its mzXML version). Not sure if that colors your
thinking. It's RAMPAdapter doing the heavy lifting.
Brian
On Mon, Oct 5
You probably mean mzXML rather than mzML?
On Fri, Oct 2, 2009 at 3:55 PM, Zhi Sun z...@systemsbiology.org wrote:
I just mean the mzML format itself. I used ReAdw to convert RAW file to
mzML
format.
Thanks,
Zhi
-Original Message-
From: spctools-discuss@googlegroups.com
Would that retain elution time information? That's important for many types
of analysis.
On Thu, Oct 1, 2009 at 5:56 AM, ChargedPeptide malm.e...@gmail.com wrote:
Hmmm...
Just a thought, while I haven't used it myself , what happens if you
try to take the route of first exporting a PKL file
It also depends to some degree on what kind of data it's coverting. For
example, in some cases it has to root through the raw mass spec data files
to recover retention time info that didn't get passed through Mascot. It's
hard to generalize.
Brian
On Mon, Sep 28, 2009 at 7:55 AM, Matthew
I'd be happy to look at a much smaller but otherwise similar data set for
any clues - you can send to ftp://insilics.serveftp.net/pub
Brian
On Mon, Sep 28, 2009 at 8:08 AM, Andreas Quandt quandt.andr...@gmail.comwrote:
hi matt,
this was also my first thought but the memory usage was at about
oops, typo
ftp://insilicos.serveftp.net/pub
On Mon, Sep 28, 2009 at 8:13 AM, Brian Pratt brian.pr...@insilicos.comwrote:
I'd be happy to look at a much smaller but otherwise similar data set for
any clues - you can send to ftp://insilics.serveftp.net/pub
Brian
On Mon, Sep 28, 2009 at 8
like this:
/usr/local/apps/tpp/bin/Mascot2XML
/IMSB/results/workflow/188/mascot_createAscFile/125380469701.dat
-D/IMSB/data/databases/swissprot_57.7/sp_9606.fasta -E trypsin -Ip
cheers,
andreas
On Mon, Sep 28, 2009 at 5:01 PM, Brian Pratt brian.pr...@insilicos.comwrote:
It also depends
I'd say just run TPP on a different computer than SEQUEST if you suspect a
bad interaction, at least until you're convinced that the stability issues
aren't with SEQUEST.
For what it's worth, TPP should probably be able to use the same Perl as
SEQUEST now. In previous versions TPP was quite
You're running into the usual Apache timeout problem on large jobs, and
running from the commandline is actually an excellent workaround. Actually
you can very properly view the web UI as a training tool for the use of
command line tools.
Brian
On Wed, Sep 23, 2009 at 10:07 AM, Kris
You only need Apache if you want to use the web-based nice user interface to
help you find your way around the TPP tool set. If you want to just run
from the command line then it's not required.
On Sun, Sep 20, 2009 at 9:59 PM, sunsun szy3...@gmail.com wrote:
HI, Can anybody here explain why
:
That doesn't make any difference.
On Aug 27, 8:12 pm, Brian Pratt brian.pr...@insilicos.com
wrote:
Yeah, that's what we use here too. Perhaps you could try it as
a different,
newly created user? It sounds like there is something peculiar
about your
shell setup
My guess is its nothing you're doing wrong - iProphet is still pretty new
and it's probably confusing the PepXMLViewer parser. If you can upload the
file that crashed pepXMLViewer to ftp://insilicos.serveftp.net/pub I Natalie
or I will be happy to have a look.
Brian
On Fri, Sep 18, 2009 at 6:47
Have a look at the decoyfasta tool that ships with TPP.
On Fri, Sep 18, 2009 at 10:21 AM, rhodea rho...@gmail.com wrote:
Dear friends,
I have a large protein database (2G) in fasta format. I want to use it
as decoy database during protein identification and append it to a
target database.
I'll have a quick look at this.
Brian
On Thu, Sep 17, 2009 at 12:13 AM, YAN ms006z...@hotmail.com wrote:
Hi everyone!
Here are some more supplementary information from the output screen of
TPP:
Command 1
c:\Inetpub\tpp-bin\ProteinProphet c:/Inetpub/wwwroot/ISB/data/
It appears to have never been run though peptideProphet.
I should add a bit of logic to proteinProphet to catch that and issue a more
useful error message.
On Thu, Sep 17, 2009 at 10:52 AM, Brian Pratt brian.pr...@insilicos.comwrote:
I'll have a quick look at this.
Brian
On Thu, Sep 17
Or maybe it just wants windows-y path descriptions? \ instead of / ?
On Tue, Sep 15, 2009 at 11:48 AM, Natalie Tasman
natalie.tas...@insilicos.com wrote:
Is it possible for you to completely uninstall your old version of
Apache, and then rerun the TPP installation? This should install, and
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