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 <[email protected]> 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 [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 -~----------~----~----~----~------~----~------~--~---
