You can directly convert thermo RAW files to mgf using *msconvert. *Why go through the trouble of converting to mzXML and then to mgf.
You can follow the thread's link below for more details. http://groups.google.com/group/spctools-discuss/browse_thread/thread/a5aae3bb8a79c20e/c9d36a54ea33a338?lnk=gst&q=msfilereader#c9d36a54ea33a338 <http://groups.google.com/group/spctools-discuss/browse_thread/thread/a5aae3bb8a79c20e/c9d36a54ea33a338?lnk=gst&q=msfilereader#c9d36a54ea33a338> Regards, *Amit Kumar Yadav * Senior Research Fellow (SRF-CSIR) IGIB, New Delhi (India) *MassWiz Web server* <http://masswiz.igib.res.in> * <http://masswiz.igib.res.in>**MassWiz sourceforge project*<https://sourceforge.net/projects/masswiz> * <https://sourceforge.net/projects/masswiz>**MassWiki*<https://sourceforge.net/apps/mediawiki/masswiz/index.php?title=MassWiki> On Thu, Sep 16, 2010 at 1:41 AM, Matthew Chambers <[email protected] > wrote: > What do you mean "it's already in cygwin" ? Just run msconvert without > arguments to get version information at the bottom. But I didn't even > realize you were running in cygwin. Did you try running it from the default > cmd.exe prompt? > > -Matt > > > > On 9/15/2010 3:07 PM, chunchao wrote: > >> Definitely, 2 dashes. My OS is windows XP. I don't know the version of >> msconvert because its already in cygwin. >> >> On Sep 15, 3:50 pm, Matthew Chambers<[email protected]> >> wrote: >> >>> Are you sure you put two dashes? You will get that error if you only >>> put one dash. If you're putting two dashes and still see that error, >>> something very odd >>> is happening. If that's the case, what version of msconvert? Is it a >>> non-English Windows? Are the localization settings set to something other >>> than the default? >>> >>> -Matt >>> >>> On 9/15/2010 2:36 PM, chunchao wrote: >>> >>> >>> >>> yes, I did. >>>> For msconvert --mgf yourfile.mzXML, it says unkown option -m.- 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.
