Matt, Thanks for your comments. Unfortunately the pkl format doesn't retain any scan numbering or retention time information. I've tried comparing the output, but it's pretty much impossible to match things up. Trying to match precursor masses to compare associated MS/MS spectra doesn't work, due to the PLGS mass correction resulting in different precursor masses in the pkl vs mzXML, even if the RAW file is lockmass corrected with MassLynx prior to mzXML conversion. Thanks for the offer of having a look though.
Nice to hear that PLGS should feature mzML export soon. We're eagerly awaiting PLGS 2.4 for many reasons. A new Aglient QTOF arrives here soon, and the Waters machine will then most likely be used mainly for label-free MSe work with PLGS, but would be nice to have the option of putting Waters DDA data through our pipeline. We now have 5 instruments from 5 different vendors... all good fun! Many Thanks, DT Matt Chambers wrote: > It usually comes down to spectrum processing - specifically scan > combination, deisotoping, and centroiding. MassWolf and msconvert are > unlikely to be able to do as well as the vendor's own processing without > significant effort devoted toward optimizing on that platform. I'll take > a look at the data if you want: I'd compare the results of the PKL > export (assuming they are named in a way that retains function/scan > information, or at least retention time) to msconvert's mzML export > (which I know preserves function/scan information) to try to determine > what is the difference in processing of the data. I know they're working > on an mzML export for PLGS; if they preserve scan combination metadata > in their output then that would be a great help as well. > > -Matt > > > dctrud 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 -~----------~----~----~----~------~----~------~--~---
