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]> 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]>> 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]>> >> >> 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]>. >> >> 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. 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.
