To search MS3 spectra in Comet, you need to set the parameter "ms_level = 3". Typically the value of that parameter is set to "2" for MS/MS scans.
http://comet-ms.sourceforge.net/parameters/parameters_201402/ms_level.php Although a few of the ProteoWizard devs are here too, you might consider sending your msconvert issue to their support list: [email protected] - Jimmy On Fri, Oct 3, 2014 at 9:14 AM, Will Fondrie <[email protected]> wrote: > Hi all, > > We have a RAW file that was collected using MS3 on an Orbitrap Fusion, and > I have a couple questions about processing it. > > First, what is the best way to convert the RAW file to mzML, so that it > can be searched with Comet or one of the other TPP search engines? I've > tried using the latest version of msconvert (ProteoWizard 3.0.6736) but I > get an error: > > processing file: 09222014_005.raw > writing output file: .\09222014_005.mzML > Error writing run 1 in "09222014_005.raw": > [ScanFilter::parse()] error parsing "FTMS + p NSI sps d Full ms3 > 380.1937@cid35. > 00 [email protected] [100.0000-500.0000]": bad lexical cast: source type > value could not be interpreted as target > > Also, after converting the RAW file, are the any special parameters I > would need to set in order to search it with Comet? > > Thank you for your help. > > Best, > Will > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
