PKL doesn't retain scan time or scan number. In Dave Trudgian's, case, it's also merging lots of raw scans without recording which ones and it's repeating the same fragments many times (at least in the sample he sent me). It's a nightmare, really: there's no regard for keeping track of the original spectral evidence. I'd like to get a look at the XML export from PLGS because I think that's much more likely to have a tolerable level of metadata. Dave said he'd get those files to me after he gets back from HUPO, but if anyone else has examples of that export I'll look at them.
-Matt Brian Pratt wrote: > Would that retain elution time information? That's important for many > types of analysis. > > On Thu, Oct 1, 2009 at 5:56 AM, ChargedPeptide <[email protected] > <mailto:[email protected]>> 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 > > <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] > <mailto:[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 -~----------~----~----~----~------~----~------~--~---
