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]> 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]> >> 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]. > 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.
