Problem solved, it was just a silly mistake on my part. It turns out my system's PATH pointed to an older version of msconvert. I changed that and now it is working perfectly.
Best, Will On Tuesday, October 7, 2014 2:49:04 PM UTC-4, Will Fondrie wrote: > > 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] >> >> - 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.
