Hi Dave, An option could be to run PLGS and then convert the PLGS XML files to mzML using the Proteios SE converter. Using this workflow the spectrum ids and retention times are retained. However, the level 1 MS data is lost, so it might not be ideal for your workflow, apart from the identifications. But you'll probably gain lock mass correction and spectrum summing, compared to the massWolf workflow. The standalone converter is found here: http://dev.thep.lu.se/fp6-prodac/browser/trunk/mzML/mzMLconverters.zip The input PLGS XML files are found in subdirectories of the PLGS project directory, and are all named MassSpectrum.xml. Here is a perl script that renames the PLGS files to the name of the raw data files: http://www.proteios.org/trac/wiki/GelBasedReport
Regards Fredrik 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 -~----------~----~----~----~------~----~------~--~---
