Hi Tamanna,
Glad that worked. The difference in the screenshots you sent is that for
the one labeled condition.jpg, the normalization you specify is for the
peptide-level quantification, and the other is for the one at the protein
level.
We recommend that at the peptide level you normalize agains
MGF doesn't support MS1 spectra with metadata (i.e. retention time). Why
do you need to convert to MGF for "MS-chromatograms"?
-Matt
Ilya.Agron wrote:
> Hi!
> We need to convert mzXML to mgf files for MS-chromatograms without
> tandem mass-spectrometry (MS1 or msLevel=1). Is it possible with T
Thanks Luis. It created 8 channels as you suggested and it worked.
I have couple more questions about the condition file and the
quantitation. I uploaded 2 files, condition.jpeg (for 8-plex) and
libra.jpeg so that I can explain my question better.
If you look at the condition.jpeg file there's an
Hello Tamanna,
I'm not sure if this answers part of your question, but I just want to
point out that you can selected either absolute or normalized display
of Libra information from within the pepXML viewer. You could then
export the desired data to a spreadsheet for whatever custom analysi
Hi Tamanna,
First, make a backup of the file C:\Inetpub\tpp-bin\tpp_gui.pl just in
case anything goes wrong and wish to go back to the original file. (I am
assuming you are using the Windows version of the TPP). Then, open this
file in Notepad (or your favorite text editor) and look for this p
Hi Luis,
Thanks. Please let me know the codes I will have one of our programmers look
into this. Also I am interested in exporting the absolute values and
normalizing from there. I would like to get the proper calculation method
for that, if you or someone else can help me with that.
Thanks
Tamanna
Hi Illya,
MsXML2Search is the current version of the TPP tool that does this
(MsXML2Other is retired).
It's included with the TPP, and you can see all of the options by
running this program without any arguments. To specify MS level
besides the default of 2, use the -M option.
Please let
Hello Tamanna,
At the moment you will need to run Libra on the command-line with the
appropriate normalization option. You can otherwise choose some other
channel, import the results into Excel, and re-normalize there.
This is a very simple fix for us, so look for an updated version of Petunia
in
Hello,
I would like to choose channels to normalize Libra values for 8-plex
iTRAQ data. I see there are only 4 channels available in the drop down
menu to choose from (under 'Libra quantitation options' right before
run analysis option) . For this data I am working on my control is
labeled with 12
Hi!
We need to convert mzXML to mgf files for MS-chromatograms without
tandem mass-spectrometry (MS1 or msLevel=1). Is it possible with TPP
mzXML2Other?
Because it doesn't work at all, it starts, processes smth and then
makes empty .mgf-files...
Or what may advise something?
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