Since option of --MSe was used in running MassWolf, the msLevel was correctly assigned to the output file of mzXML. The problem could be due to the missed link between precursor ion and ms/ms spectra as Eng pointed out that it may need Waters IdentityE to do the job or need additional codes to convert mzXML to .mgf in current TPP soflware.
What I am trying to do is protein identification using MSe mode and processing data with open source software. The reason I did not use PLGS is that it will cost about $13000 to buy the software. The other option to use MSe data for protein identification is msInspect --> mascort as demonstrated by R.S. Philosof in his Master Thesis (http://www.gelifesciences.com/aptrix/upp00919.nsf/Content/ 689F675DA7323088C1257628001CCFF3/$file/52130800BB.pdf). However, msInspect is run under Java and R. The installation seems complicated and I don't have any knowledge on R. I have not tried it. I will try msconvert to see if it works. Thank you all for helpful suggestions. On Apr 11, 8:31 pm, Jimmy Eng <[email protected]> wrote: > 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 <[email protected]> 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 [email protected]. > > To unsubscribe from this group, send email to > > [email protected]. > > For more options, visit this group > > athttp://groups.google.com/group/spctools-discuss?hl=en.- 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]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
