Dear all, another query r.e. Waters QTOF data.... We have a QTOF Premier which is now being used for SILAC experiments, and we want to quantify using ASAPRatio / Xpress. Have no problems doing this in our pipeline using Orbitrap data, but the QTOF data is causing headaches. Up until now we've mostly been using MassWolf just to get MS data into .mzXML for purposes other than ID & quant, PLGS having been the preferred analysis tool for the instrument.
If we use .mzXML files and feed them to Mascot/OMSSA/Tandem + TPP we cannot get anywhere near the number of IDs as with .pkl files generated using PLGS. We've tried conversion to mzXML using MassWolf and msconvert, applying lockmass correction in MassLynx prior to conversion, and comparing acquisition of MS/MS scans in centroid mode, vs acquisition in profile mode converted to centroid using MassLynx. An example of the differences in IDs: RAW->PLGS->PKL->Mascot->TPP: 874 peptide IDs (1% FDR) RAW->MassWolf->mzXML->mgf->Mascot->TPP: 279 peptide IDs (1 % FDR) No matter what combination of converter / pre-processing in MassLynx we try, the number of IDs is never above 1/3 of that we get from a PKL file. We've also tried changes to the acquisition methods, without success. Is anyone able to provide a MassLynx method file, and/or procedure for pre-processing / .mzXML conversion they are using successfully with a QTOF Premier or similar instrument? Any help would be gratefully appreciated. Many Thanks, DT --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
