msconvert: polarity negative/positive

[Cédric]

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, Cédric

[Matthew Chambers]

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
>

[Cédric]

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 <matt.chamber...@gmail.com>
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

[Matthew Chambers]

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, C�dric 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

> C�dric

[Cédric Bovet]

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 <matt.ch...@gmail.com> 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<matt.chamber...@gmail.com>
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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[Matthew Chambers]

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, C�dric 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, C�dric

>
>
> On 29 March 2011 18:58, Matthew Chambers <matt.ch...@gmail.com

> <mailto:matt.ch...@gmail.com>> 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, C�dric 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

> C�dric

>
> On Mar 29, 5:45 pm, Matthew Chambers<matt.chamber...@gmail.com

> <mailto:matt.chamber...@gmail.com>>

> 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
>
>
>
> --
> You received this message because you are subscribed to the Google Groups "spctools-discuss" group.
> To post to this group, send email to spctools...@googlegroups.com

> <mailto:spctools...@googlegroups.com>.

> To unsubscribe from this group, send email to spctools-discu...@googlegroups.com

> <mailto:spctools-discuss%2Bunsu...@googlegroups.com>.

[Cédric Bovet]

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

Do you have another suggestion? Thanks, Cédric

On 29 March 2011 18:58, Matthew Chambers <matt.ch...@gmail.com

<mailto:matt.ch...@gmail.com>> 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

[Matthew Chambers]

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, C�dric 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?

> C�dric

>
> Here are the cmd lines that I got
>
> On 30 March 2011 16:42, Matthew Chambers <matt.ch...@gmail.com

> Do you have another suggestion? Thanks, C�dric

>
>
> On 29 March 2011 18:58, Matthew Chambers <matt.ch...@gmail.com
> <mailto:matt.ch...@gmail.com>

> <mailto:matt.ch...@gmail.com <mailto:matt.ch...@gmail.com>>> 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, C�dric 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

> C�dric

>
> On Mar 29, 5:45 pm, Matthew Chambers<matt.chamber...@gmail.com
> <mailto:matt.chamber...@gmail.com>

> <mailto:matt.chamber...@gmail.com <mailto:matt.chamber...@gmail.com>>>

>
> 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
>
>
>
> --
> You received this message because you are subscribed to the Google Groups
> "spctools-discuss" group.
> To post to this group, send email to spctools...@googlegroups.com
> <mailto:spctools...@googlegroups.com>

> <mailto:spctools...@googlegroups.com <mailto:spctools...@googlegroups.com>>.

>
> To unsubscribe from this group, send email to
> spctools-discu...@googlegroups.com
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> <mailto:spctools-discuss%252Buns...@googlegroups.com>>.

[Cédric Bovet]

Matt, thanks a lot for your help, that's working now! Regards, Cédric

On 30 March 2011 17:33, Matthew Chambers <matt.ch...@gmail.com> wrote:

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

       Do you have another suggestion? Thanks, Cédric

       On 29 March 2011 18:58, Matthew Chambers <matt.ch...@gmail.com
       <mailto:matt.ch...@gmail.com>

       <mailto:matt.ch...@gmail.com <mailto:matt.ch...@gmail.com>>> 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