It's a software problem on a couple of levels. ReAdW was never
intended for gcms data so it was never tested on those instruments and
I would be surprised if it worked. Additionally, most if not all of
the software tools that consume mzXML files probably won't work with
the data, even if you
Sequest search engine.
with best regards
Blacky
On 22 Feb., 18:13, Jimmy Eng jke...@gmail.com wrote:
Die pepXML Akte ist zu klein. Es gibt keine Suchresultate in der Akte.
Fokus auf, wie diese Akte erzeugt wurde.
(I thought it would be cute to reply in German. The above is a babel
fish
Maybe try the Thermo RAW to imzML converter software in this link;
looks like BioMap supports imzML input.
http://www.maldi-msi.org/index.php?option=com_contentview=articleid=189Itemid=69
On Wed, Feb 24, 2010 at 12:15 PM, Andrew a.har...@usip.edu wrote:
I am trying to convert the actual raw
Robert,
You need an mzXML file present in order for the spectrum viewer and
Pep3D viewer to work. Both of those reads the spectrum data from that
file. Additionally, the various files (pep.xml, base_name attribute
in the pep.xml, mzXML, etc.) must follow a standard convention for it
all to work
Christian,
readw is and will always be a windows app because it makes use of
windows DLLs supplied by Thermo to read the raw files. If you really
want to get away from the data transfers (which you can automate ...
search for 'conversion server' on this group to see Greg Taylor's
recipe for
The 672.3157959 mass is likely from the scan header in the raw file
for that particular scan. Open up the raw file in qualbrowser and
take a look at the scan header and see what the monoisotopic m/z
value is. (Hopefully it's 672.3157959).
This would just explain the discrepancy. Why the m/z
Ludovic,
Given that you're looking for 5+/6+ peptides, can you check to make
sure the peptide masses are not above the high mass cutoff default
(4200 Da) for MzXML2Search? If so, you would use the -T option to
specify a higher mass cutoff e.g. MzXML2Search -mgf -T8000.0
file.mzXML
- Jimmy
On
The patch was added as revision 4777. Works for the sqt file I have
access to but someone should still test with whatever sqt files were
causing the problem in the first place. Note I felt obligated to also
change the output extension from .pepXML to .pep.xml to conform with
all of our other
In a gross simplification, PeptideProphet fits positive and negative
distributions to the overall search results distribution as part of
its processing to calculate probability scores for each
peptide-to-spectrum match. That checkbox you're referring to tells
PeptideProphet to use the decoy
I'll add the substitutions to the getdb.* scripts in the TPP src/util directory.
Should a substitution be added to the IPI retrieval utility scripts in
the TPP distribution so that the problem doesn't show it's face if
they are being used?
jimmy and greg,
i was not aware that each directory has to be processed individually but i
agreed this can be wrapped up in a script ;-)
but i tried the command greg suggested and still get the segmentation fault
:-(
cheers,
andreas
On Fri, Oct 2, 2009 at 8:49 PM, Jimmy Eng jke
TPP 4.3.1 install includes the installation file
c:\inetpub\tpp-bin\trapper_setup.exe
Double click on that setup file which installs trapper.exe into
c:\Program Files\trapper\ along with the appropriate libraries. Then
try your conversion referencing the installed trapper.exe executable.
On
I'll be a translator. Zhi seems to be having issues with ABI QQQ wiff
files. They were translated to mzML using msconvert and X!Tandem
didn't like them. She mentioned ReAdW only to state that X!Tandem was
able to process some unrelated mzML files in the past.
The problem could be:
1) the QQQ
Ian,
The quick test is to repeat the search using your older files with the
newer TPP install. Use the same search parameters as you did before.
If you get your 300+ identifications then the problem is likely with
your new data files. If you don't get the expected number of IDs as
you got
If you run the Sequest search through the TPP GUI interface or via the
runsearch.exe wrapper on the command line, it would pack up and
compress the search results folder and delete the corresponding
directory (of dta/outs). You obviously don't need to keep the folders
around if you have no use
#2. see http://www.thegpm.org/TANDEM/api/refpctm.html
I hate to state the obvious but this will only be applied in
refinement mode so make sure that's turned on.
On Wed, Sep 16, 2009 at 2:44 PM, rhodea rho...@gmail.com wrote:
Dear friends,
If I want to use the following PTM:
Monoisotopic:
and hence would be good if an XML file
can be created for such experiments.
Please let me know.
Thanks and regards,
~Nikhil Garge
Biostatistics analyst
RTI International
Durham NC 27709
Email: nikhil.ga...@gmail.com
Phone: 919-541-5902
On Fri, Sep 4, 2009 at 10:18 PM, Jimmy Eng jke
Of Jimmy Eng
Sent: 04 September 2009 19:13
To: spctools-discuss@googlegroups.com
Subject: [spctools-discuss] Re: problem for the tpp ananlysis with indexed
database
Eileen,
It should work. As Brian suggested, post the error/log message so
that we can see what the problem actually is to help
That 742.5391 precursor mass is the monoisotopic m/z mass recorded in
the scan header of the raw file itself. readw just grabs this value,
if present, via the thermo interface. No way to turn this off in
readw (besides a relatively simple edit of the code and rebuilding the
binary).
Without
There's a search parameter (print_duplicate_references) which defines
printing out the additional protein references that a peptide matches.
Should be a straightforward fix to Out2XML to handle these files
(which I'll look at next week when I get back if no one has updated
the program by that
Unfortunately you'll need to edit and recompile runsearch1.c (around
line 165) which is in the TPP's src/util/ directory. Follow up here if
that's something you need assistance with.
Kris wrote:
Hi everyone,
I've searched the forums, but I can't seem to find where you specify
the path
Is there a chance the lower intensities are due to isotopic correction
being applied? What are the correction values in the condition.xml
file you used.
lgillet wrote:
Hi,
We have realized some inconsistency in the intensitites reported by
Libra on TPP (v4.0 JETSTREAM rev 2, Build
with the installation. I will have to reinstall/
rebuild the computer.
Antonio
On Jul 9, 2:41 pm, Antonio aartig...@kumc.edu wrote:
Ok Jimmy,
Thank you very much for your help.
I'll repeat the entire process from TPP and I will let you know the
result.
Regards,
Antonio
On Jul 9, 2:18 pm, Jimmy Eng j
.
-Original Message-
From: spctools-discuss@googlegroups.com
[mailto:spctools-disc...@googlegroups.com] On Behalf Of Jimmy Eng
Sent: Wednesday, July 15, 2009 10:26 AM
To: spctools-discuss@googlegroups.com
Subject: [spctools-discuss] Re: pepXML
Antonio,
Hopefully Luis or someone else more
.
- Jimmy
Antonio wrote:
Hi Jimmy,
OK, done it. No problem, the command were successfull, all finished,
th eTPP window indicated that the command was sucessfull and is
finished. i can open the basename.pep on TPP and all seens OK.
What next?
Antonio
On Jul 8, 12:33 pm, Jimmy Eng j
files or a
single one. But I have more than one file on the queue, the command
will not proceed to the next file. I can run Sequest from Bioworks on
the local machine without any problems.
On Jul 2, 6:55 pm, Jimmy Eng j...@systemsbiology.org wrote:
Antonio,
That warning about not being
Bernt,
The good news is that you shouldn't need to re-run Tandem searches to
address this problem.
The easiest way that I can think of to help you is to show you the
convention of file names, base_name attributes, and paths that the tools
typically expect/generate.
directory of data:
FYI - I've run MassWolf on Vista many times. Just did it again with the
4.2.1 version and it worked fine.
Natalie Tasman wrote:
Hi MIchelle,
This program was not tested under Vista, and I'm not sure if it
works. I recommend XP or 2003 if you have access. But some quick
checks: do
name=expect value=0.168173793062284/
/search_hit
On Jul 2, 4:44 pm, Jimmy Eng j...@systemsbiology.org wrote:
Ping,
I just downloaded OMSSA 2.1.4 and tried the direct pep.xml export
myself. I do see a problem with the resulting pep.xml file that the
-op option generates that's causing
Ping,
I just downloaded OMSSA 2.1.4 and tried the direct pep.xml export
myself. I do see a problem with the resulting pep.xml file that the
-op option generates that's causing the problem you're seeing.
The key error message in your output is this:
WARNING: No decoys with label DECOY were
iTRAQ is quantified based on ms/ms fragment peaks; use the Libra tool
for that labeling method. ASAPRatio and XPRESS are not meant to work on
iTRAQ data.
As for O18 labeling, under the presumption that two O18 atoms are
incorporated into the heavy labeled peptides, you want to specify a 4 Da
Bright,
See slide 59 of the Day 4 lecture by David titled XPRESS and ASAPRatio
available on the web page below. That slide describes that the numbers
mean.
http://www.proteomecenter.org/course.php
Both sets of numbers are light:heavy ratios and corresponding standard
deviations. The
Greg,
You need to update gnuplot. Do latest 4.2.2 if you can; possibly 4.1.x
will work also. There's new gnuplot syntax used that's not backwards
compatible with gnplot 4.0.
- Jimmy
bowers...@gmail.com wrote:
It looks like I am having an issue with gnuplot or one of the calls to
it now.
XPRESS has no functionality to handle partial incorporation. If the
partial incorporation manifests itself as ratios that need correction,
you'll have to do that correction separately.
- Jimmy
Leticia Lery wrote:
Hi, I need some help to analysis of 15N Metabolic Labeling.
I´ve some
the Sequest search. I am wondering if this is causing the
problem. If this is the cause, do I need to do the Sequest search over
again without using the indexed database, or is there anything else I
can do to solve the problem?
Thank you,
Xin
On May 1, 4:12 pm, Jimmy Eng j...@systemsbiology.org
Xin,
You might be choosing the wrong file as input. ProteinProphet requires
a *.pep.xml file that contains PeptideProphet probabilities and these
usually have file names like interact*.pep.xml. The file names below
seem to imply that you're choosing the wrong pep.xml file as input.
Your
Ben,
Your best place for help with running X! Tandem from the command line is
probably the GPM's website.
helpful links:
http://www.thegpm.org/tandem/tandem_install_faq.html
http://www.thegpm.org/TANDEM/api/index.html
You need some input xml parameters file. Such a file would contain
Xin,
You shouldn't have to run separate searches. Your attached images where
the mzXML file name is XW3127C3OUT.mzXML implies that there's an error
in the file name encoding somewhere. Presumably the file should be
XW3127C3_090129.mzXML.
Feel free to send me your pep.xml file and I'll take
Mattias,
I just checked in the Xpress changes to trunk (revision 4331). Give it
a shot and let me know if there's any problems.
There was mention of 15N support in ASAPRatio in the 4.2 announcement.
After doing more snooping, the following check-in added support for
initializing AA masses
What file did you truncate to 10MB? Your individual dta and out files
should be pretty small.
You haven't supplied enough information such that anyone here could
identify the cause of your problems. Here's what I would suggest:
1) copy your .params to be named sequest.params and place it
On Mar 21, 12:21 am, Jimmy Eng j...@systemsbiology.org wrote:
Henry,
I'm not going to have any time in the next week or so to look in to the
problem. But your interpretation of what deltaCn means is wrong or
rather different than what it is meant to represent.
The premise for the ad-hoc
Kris,
Is your search parameters file named sequest.params or
PAe000144_414_sequest.params?
If it's not sequest.params, this would explain the behavior. You're
able to specify a different name for the parameters file to run a search
but the downstream tools (i.e. Out2XML) aren't that
Camilo,
Can you look into the *.pep.xml file and report what the base_name
attribute values are?
You can fine them in lines that look like:
msms_run_summary base_name=SOME_NAME ...
search_summary base_name=SOME_NAME ...
What is in the SOME_NAME field? And where does the mzXML file
don't have the
Sequest executable on my machine. I received the data from our
collaborators who have XCalibur installed on theirs. If I just
requested the .pep.xml from them, could I still analyze the data or
would other output files from sequest be needed?
-Amanda
On Dec 19, 11:57 am, Jimmy
The program cannot find the mzXML file(s) to read chromatograms and
calculate ratios. w/o more details, it's hard to know where the problem is.
[EMAIL PROTECTED] wrote:
Hi,
I didn't find this topic in the archives, and was wondering if we
could get some help. XPressPeptideParser seems to
Josh Eckels
if he knew what was breaking. I assumed it was cpas as well. He
suggested I post here, saying:
...Jimmy Eng, the main xpress guy, monitors the
list and will hopefully be able to lend a hand.
Since the system doesn't break except on these files, regardless on
name; and because
ICPL labels lysine residues at the protein level and quantification
happens in the MS1 scans. So ASAPRatio can quantify that data just like
SILAC or ICAT.
If I had to guess, Sara's problem with ASAPRatio and her Mascot searches
are possibly due to issues with losing connectivity between scan
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