Thank you Jimmy, I'll submit my problem to the msconvert support list. When I hear back, I'll make sure to update here with the answer as well. I'm glad to know that it won't be a problem searching with Comet.
Best, Will On Friday, October 3, 2014 1:14:23 PM UTC-4, Jimmy Eng wrote: > > 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] <javascript:> > > - Jimmy > > On Fri, Oct 3, 2014 at 9:14 AM, Will Fondrie <[email protected] > <javascript:>> 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] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> 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.
