Hi,
I'm performing TPP analysis for my 14N/15N metabolic labeling
experiments and have some questions regarding the data processing
steps:
The raw data were searched one time with the normal 14N masses, and
once with the 15N enriched amino acids set as fixed modification by
Sequest in the
Dear all
I am an absolute newbie and I am not sure if I came to the right
place... well, here's my question:
I am looking for a tool that extracts chromatogram data from XCalibur
*.raw files and converts them into a format that is readable by other
software (e.g. Matlab or Octave). My *.raw
Hi Jimmy,
thanks for the quick reply.
1.) Is it possible to use 13C labeling with either XPress or
ASAPRatio? I've found only options for 15N, so is there any chance to
process 13C-labeled samples?
You can't analyze 13C labeling now with Xpress. I don't see 13C (nor
15N) support
ProteoWizard's msconvert will almost work for this. If you give me an
example RAW file I can fix it up rather quickly. ReAdW isn't close to
being able to support this, not least because mzXML doesn't support
chromatograms (and it's also entirely about mass spectra). I have tested
msconvert on
The great thing about TPP, of course, is that it's open source. So, you've
already got source code and MSVC build files for readw, which shows you
exactly how to use the Thermo DLLs.
After that, well, Google is your friend!
Begin here:
https://sashimi.svn.sourceforge.net/svnroot/sashimi/trunk
Hi Mattias,
To get started with Xcalibur, you might want to look at the XDK for
examples.
But I do think it will be easier if you can just use and/or adapt existing
tools. I know that Matt from the ProteoWizard (PWIZ) project (including in
the TPP) has been interested in parsing chromatogram
Hi Matthias,
[Looks like some other folks might be able to help you out directly;
take the below with a grain of salt]
Most of the folks here work with LC not GC MS. However, the existing
software for extracting LCMS data should at least get you started
towards your own. I would start with
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
Luis,
I finally got my PepXMLViewer working. I opened the file, and there is
no entries with exact zero
probability. But there are tons of entries with ~0.05 probability.
Does that matter? Or QualScore
only considers that zero probability as bad spectra?
The data is LTQ data, and first is
Hello Ping,
Yes, please make sure you run xinteract with the -p0 (zero, not O)
option. QualScore uses those to model the bad spectra.
--Luis
On Thu, Apr 16, 2009 at 10:43 AM, Ping yanpp...@gmail.com wrote:
Luis,
I finally got my PepXMLViewer working. I opened the file, and there is
no
Hi Angel,
I have setup some proteomics tools running on parallel on a Linux
cluster here at the Beckman Research Institute of City of Hope Medical
Centre.
I am not sure what you are looking for exactly: student, postdocs,
collaboration or consultation.
But if there is anything I can do to help,
I'm using TPP 4.2.0 to analyze cleavable ICAT data from an LCQ. When
all replicates are done, I have 120 seperate .pep.xml files to combine
and analyze. With earlier versions of TPP (i.e. 3.4) I could analyze
them all at once with Xinteract, but with 4.2 the operation simply
aborts and fails
Hi,
Long time ago there was an option to save a subset of a pepXML (for
example only peptides with ratio 2) to a new pepXML file through the
GUI but I haven't seen it for a while. Is it still possible to it with
the latest TPP though the GUI (or by using the command line somehow).
Thanks for any
There's not meant to be a limitation - can you give an example of a command
line that fails?
-Original Message-
From: spctools-discuss@googlegroups.com
[mailto:spctools-disc...@googlegroups.com] On Behalf Of Kristian
Sent: Thursday, April 16, 2009 11:56 AM
To: spctools-discuss
Subject:
Hi Oded,
You are correct; this was a feature with a very old version of the pepXML
display that isn't currently active. The current viewer is strictly
read-only, so far. This hasn't been a very high priority so far as
xinteract and the prophets do the most common filtering (probabilities), but
Hi Kristian,
Also, 4.2.1 contained many bug fixes. I'm not sure if this would have been
addressed, but it's always most efficient for us if you can try to replicate
the issue on the latest version.
-Natalie
On Thu, Apr 16, 2009 at 12:42 PM, Christine Vogel vogel@gmail.comwrote:
I have
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 lmend...@systemsbiology.org wrote:
Hello Ping,
Yes, please
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