Hi, I would like to continue this discussion, because I still have problems with RTs.
I have a combined mgf file, from 30 different SCX fractions. The title should be correct, as it used to work with a single file. It is in the format: BEGIN IONS PEPMASS=616.869977288255 CHARGE=2+ and 3+ TITLE=OR2_090730_JR_PLacLysN_SCXfrac11.782.782.0 I have put all mzXML files in the same directory as the dat file and run Mascot2XML Mascot2XML.exe C:\Inetpub\wwwroot\ISB\data\Jeffery_RT\TrypSCXa \F264728_TrypSCXa.dat -DC:\Inetpub\wwwroot\ISB\data\Jeffery_RT\TrypSCXa\mydatabase.fasta -Estricttrypsin -notgz Even like this, I could not get RT info in my pepXML and Mascot2XML was complaining that it could not find the combined mzXML warning: cannot open "c:/Inetpub/wwwroot/ISB/data/Jeffery_RT/TrypSCXa/ F264728_TrypSCXa.mzXML" for reading scan numbers. Are you sure that mascot2XML can work out which mzXML file to look in ? Thanks, Salvo On Nov 5, 5:42 pm, dctrud <[email protected]> wrote: > Hi, > > You don't need the mzXML file to be present to analyse the Mascot > results with the TPP tools. You will lose certain functionality > though, such as not being able to use the XPRESS / ASAPRatio > quantitation tools for SILAC data etc. > > If you do have the mzXML files then the TPP tools work out which mzXML > file to look in by interpreting the spectrum title for each match in > the Mascot output. This spectrum title is specified as TITLE=xxxxxx in > the MGF file you submit to mascot. The TPP needs the titles to be in a > specific format. See the current thread about OMSSA for details. If > the titles are in the correct format then merging the MGF files isn't > a problem, so long as whatever method you use to merge the files > doesn't change the titles. > > Rather than merge mgfs and running a single search you can also run a > Mascot search for each mgf, and merge the results within the TPP. > > DT > > On Nov 4, 8:33 pm, Xi Qiu <[email protected]> wrote: > > > > > > > > > Dear All, > > > I am using TPP to analyze my Mascot search result which is a .DAT > > file, but when I want to convert the .DAT file to pepXML, TPP need > > mzXML file to read scanning number or something else which I do not > > remember clearly. Because I merged several .mgf files to one .mgf to > > perform the search and I think I need to merge the corresponding mzXML > > files to a big mzXML file. I wonder does any one know how to do this? > > And if it is required to have a corresponding mzXML file to be there > > to analyze the mascot result? > > > Thanks everyone for looking and I really appreciate your help. > > > Best -- 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.
