Hi Bob, If you have an mzXML or mzML file, you can also use the TPP-provided utility readmzXML. The following command pulls spectrum with scan number 123 from file.mzXML and outputs to the screen (STDOUT):
%> readmzXML -r file.mzXML 123 To see all other options and usage statement, simply type the command name (readmzXML) and hit return. Cheers, --Luis On Thu, Jan 20, 2011 at 12:39 PM, bobxiong <[email protected]> wrote: > Hi Matt, > > Specifying MGF didn't work with msconvert. > > msconvert my_fullscan.wiff --mgf > > The command above generated one output file per sample, but the files > were all empty. There was no error displayed when the process was > completed. > > After playing around with output format options, I'm happy to report > that the --text option (write ProteoWizard internal text format) > produced what I wanted, i.e. mz and intensity data for ALL peaks. (One > of the wiff files produced an error during processing. The error msg > was "Error writing run 10 in survey_fullscan.wiff: An attempt was made > to move the file pointer before the beginning of the file". The output > file contained no data as a result.) > > Thanks, > > Bob > > On Jan 20, 12:06 pm, Matthew Chambers <[email protected]> > wrote: > > > http://proteowizard.sourceforge.net/technical/tools/msconvert.htmlhttp://www.ms-utils.org/wiki/pmwiki.php/Main/SoftwareList > > msconvert: converts from > RAW/WIFF/T2D/Agilent/Bruker/Waters/mzML/mzXML/MGF/MS2 to mzML/mzXML/MGF/MS2 > > > > -Matt > > > > On 1/20/2011 11:02 AM, bobxiong wrote: > > > > > > > > > Hi Matt, > > > > > What tool can convert mzML to MGF? > > > > > Thanks, > > > > > Bob > > > > > On Jan 20, 11:42 am, Matthew Chambers<[email protected]> > > > wrote: > > >> Keep in mind that you can convert from mzML to MGF instead of WIFF to > MGF (because the WIFF reader > > >> is so slow). > > > > >> -Matt- Hide quoted text - > > > > - Show quoted text - > > -- > 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]<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.
