Would that retain elution time information? That's important for many types of analysis.
On Thu, Oct 1, 2009 at 5:56 AM, ChargedPeptide <malm.e...@gmail.com> wrote: > > Hmmm... > Just a thought, while I haven't used it myself , what happens if you > try to take the route of first exporting a PKL file and then > converting to mzXML using > PKL2MZXML <a href="http://tools.proteomecenter.org/wiki/index.php? > title=Software:pkl2mzXML">Link</a>? > I assume most of the pre processing will already have been carried out > from the raw data and the conversion is simpler, even though as I > said, I might be way of the money here. > > On Sep 14, 1:37 pm, dctrud <dct...@ccmp.ox.ac.uk> wrote: > > 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 spctools-discuss@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 -~----------~----~----~----~------~----~------~--~---
