Matt, thanks a lot for your help, that's working now! Regards, Cédric On 30 March 2011 17:33, Matthew Chambers <[email protected]> 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 >> >> 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 >> >> >> >> -- >> You received this message because you are subscribed to the >> Google Groups >> "spctools-discuss" group. >> To post to this group, send email to >> [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto: >> [email protected]>>. >> >> >> To unsubscribe from this group, send email to >> [email protected] >> <mailto:spctools-discuss%[email protected]> >> <mailto:spctools-discuss%[email protected] >> <mailto:spctools-discuss%[email protected]>>. >> >> >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> >> >> -- >> >> You received this message because you are subscribed to the Google >> Groups "spctools-discuss" >> group. >> To post to this group, send email to >> [email protected] >> <mailto:[email protected]>. >> To unsubscribe from this group, send email to >> [email protected] >> <mailto:spctools-discuss%[email protected]>. >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> >> >> -- >> You received this message because you are subscribed to the Google >> Groups "spctools-discuss" group. >> To post to this group, send email to [email protected] >> <mailto:[email protected]>. >> To unsubscribe from this group, send email to >> [email protected] >> <mailto:spctools-discuss%[email protected]>. >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To post to this group, send email to [email protected]. >> To unsubscribe from this group, send email to >> [email protected]. >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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