John, The TPP doesn't support the analysis of Spectrum Mill results. SEQUEST, Mascot, X!Tandem (native/k-score), ProbID, SpectraST, Phenyx, OMSSA, MyriMatch, Inspect, and YABSE are all possibilities though.
To use Mascot you can try converting the mzXML files to MGF for Mascot using the TPPs MzXML2Search tool and specifying a value for the -I parameter, which filters out peaks lower than a set intensity. For example: MzXML2Search -mgf -I20 my.mzXML ... will generate an mgf file from my.mzXML which exclude peaks with an intensity less than 20. This will dramatically reduce the size of the mgf file since QTOF data tends to include a lot of very low intensity noise peaks. The value you use for the cut-off depends on the instrument. Set it to something that looks reasonable for getting rid of the lowest level noise, but not useful signal. For our Agilent 6520 (ADC based) we use 20, for a Waters QTOF (TDC based) we use 3. A caveat is that direct mzXML to MGF to Mascot doesn't give great results in our hands with data from the 6520 QTOF. Mascot benefits a lot from the spectrum processing (such as de-isotoping) that is performed when exporting an MGF from MassHunter (or indeed Mascot Distiller). On the other hand, OMSSA and X!Tandem (native scoring) work extremely well for us with spectra from the mzXML. We routinely analyse 6520 data using OMSSA + X!Tandem native, with iProphet to combine the results, and use ASAPRatio successfully for quantitation. DT On Apr 13, 9:13 pm, John <[email protected]> wrote: > I want to use ASAPRatio incorporated in TPP suite. However, we do not > have Sequest and Our Mascot currently cannot read the XML files > generated by TPP because of the huge size of mzXML file after > converting Agilent Q-TOF data (.d) to mzXML file. > > I am trying to use X!Tandem in TPP suite to do database search. > However, I noticed that the X!Tandem incorporated in TPP is an old > version. Can I incorporate the latest X!Tandem in TPP? > > Can I use the latest X!Tandem to do the database searching and output > the data into a format that TPP can read for further SILAC > quantification? > > How Can I convert Spectrum Mill search result to the format TPP can > read and to perform SILAC quantification? -- 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.
