Frederik, Many thanks for this information, I hadn't come across the Proteios convertor. Unfortunately we're working now with SILAC data where we need the MS1 for quantitation, but the workflow might be useful for other data. I have previously extracted EMRT information from PLGS XML files in MS^e experiments, but hadn't thought to look at the XML files for DDA.
Thanks, DT fredrik wrote: > 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 -~----------~----~----~----~------~----~------~--~---
