The problem is likely due to MSe spectra not being labeled as MS level 2 scans (ms/ms scans) in the mzXML file. Look for "msLevel=" attribute in the file to see what MS level is assigned to these spectra. If I had to guess, they are considered MS level 1 scans and no distinction is made between low energy and high energy acquisition modes.
The bigger but not quite related question is what do you hope to accomplish by exporting MSe scans to mgf? You will need a specialized search engine like Waters IdentityE in order to analyze that type of data containing fragments from mixtures of peptides. I'll also throw in the obligatory "consider use msconvert instead of masswolf" going forward. On Mon, Apr 11, 2011 at 12:15 PM, hw <hw080...@gmail.com> wrote: > I have trouble to convert Masslynx's MSe data file to mzXML then > to .mgf file with TPP. Here is the command I used: > masswolf --mzXML --nolockspray --MSe C:\data.raw C:\data.mzXML > > The output file data.mzXML can be viewed with InsilicoView and it > looked ok. However, when TPP was used to convert .data.mzXML to .mgf, > there was no peak in it. In MSe mode, low energy was set at 2 and high > energy was set to 20-30V. I don't have much experience on Masslynx > software. Is it possible that some settings in MSe mode was not > correct? or is it possible masswolf requires some special settings? > any comment is appreciated. > > By the way, I have no problem to convert masslynx's DDA data file to > mzXML then to .mgf using TPP. Mascort search with this .mgf file > yielded positive results. In processing DDA data, masswolf command was > > masswolf --mzXML --nolockspray C:\data.raw C:\data.mzXML > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to spctools-discuss@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com. > 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 spctools-discuss@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
