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 <afrir...@gmail.com> 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 spctools-disc...@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.
