Overwrite the msconvert in the tpp-bin directory. Or use the full path to the new msconvert
executable, e.g.
c:\path\to\msconvert.exe
-Matt
On 3/30/2011 10:30 AM, Cédric Bovet wrote:
Ah, that's maybe the point. When I am running msconvert the first time in cmd,
it shows me
"ProteoWizard release 2.1.2596" at the end. After that, I runned msconvert
without args and it shows
me ProteoWizard relesae 2.1.2132". What should I do?
Cédric
Here are the cmd lines that I got
On 30 March 2011 16:42, Matthew Chambers <[email protected]
<mailto:[email protected]>> wrote:
I can't reproduce this. Are you sure about the version of msconvert you're
running?
"ProteoWizard release 2.1.2596" shows up when you run msconvert without
args?
-Matt
On 3/30/2011 1:42 AM, Cédric Bovet wrote:
Matt, I tried what you suggested. Unfortunately, it didn't work,
msconvert still told me that it
"ignores the wrapper" (see below). I am able to read the mzXML, but the
file contains both
positive
and negative ion traces. Here are the command lines and messages from
msconvert
--------------------------------------------
C:\Users\cbovet>msconvert
Z:\Toxikologie\LTQVelos\data\Cedric\CBo_1001_110315A\C
Bo_1001_110315A_03.raw --32 --mzXML --filter "analyzerType ITMS" --filter
"polar
ity negative" -o Z:\Toxikologie\MSconvert
format: mzXML (Precision_32 [ 1000514:Precision_32 1000515:Precision_32
], ByteO
rder_LittleEndian, Compression_None) indexed="true"
outputPath: Z:\Toxikologie\MSconvert
extension: .mzXML
contactFilename:
filters:
analyzerType ITMS
polarity negative
filenames:
Z:/Toxikologie/LTQVelos/data/Cedric/CBo_1001_110315A/CBo_1001_110315A_03.raw
processing file:
Z:/Toxikologie/LTQVelos/data/Cedric/CBo_1001_110315A/CBo_1001_1
10315A_03.raw
[SpectrumListFactory] Ignoring wrapper: analyzerType ITMS
[SpectrumListFactory] Ignoring wrapper: polarity negative
writing output file: Z:/Toxikologie/MSconvert/CBo_1001_110315A_03.mzXML
---------------------------------------------
Do you have another suggestion? Thanks, Cédric
On 29 March 2011 18:58, Matthew Chambers <[email protected]
<mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>>
wrote:
Interesting. That appears to be a bug in the config file reader.
Until it gets fixed,
use the
command-line equivalent for filters, i.e.
--filter "analyzerType ITMS" --filter "polarity negative"
-Matt
On 3/29/2011 11:49 AM, Cédric wrote:
Hi Matt. I used a configuration file (-c) containing the
following
information
outdir=Z:\Toxikologie\MSconvert\negmzXMLfiles
mzXML=true
32=true
filter="analyzerType ITMS"
filter="polarity negative"
for the version, it is the one contained with ProteoWizard
release
2.1.2596 (ProteoWizard MSdata 2.1.2595, ProteWizardAnalysis
2.1.2587).
Is it the information that you need? Thanks for your help
Cédric
On Mar 29, 5:45 pm, Matthew Chambers<[email protected]
<mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>>
wrote:
What was your exactly command-line and which version of
msconvert did you use?
-Matt
On 3/29/2011 3:07 AM, C dric wrote:
Hi,
I am using msconvert to transform my .raw file acquired
on a LTQ Velos
into mzXML file. I performed LC-MS measurements in
positive/negative
mode in a single run, therefore my files contain both
ion trace (i.e.,
positive and negative). I am trying to extract from my
.raw file the
negative ion trace and convert it in mzXML
(filter="polarity
negative"). When I am doing that, msconvert ignore my
filter (it wrote
back Ignoring wrapper: ) and transform my raw data into
mzXML file
which contains the negative and positive ion trace.
Does anybody know
how to extract each ion trace separately?
thanks a lot for your help, C dric
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