Hi Matt, Thanks for the explanation. Would appreciate if you could elaborate more on how periods, cycles and experiments are defined w.r.t conventional data-dependent acquisition schemes. :)
There's another problem that I observed, that in the generated mzXML file, with or without peakPicking, I could only view the m/z range of 600-800. Do you know the reason for this? This was verified using InSilicos and Pep3d. I haven't tried to convert the Sha encrypted peaks to confirm, thought it would be easier to confirm first with you. Thanks heaps for all your help! Bernt On Sep 25, 9:37 pm, Matt Chambers <[email protected]> wrote: > Msconvertshould enumerate all the non-SRM and non-SIM spectra. Due to > performance issues of the API, it enumerates cycles first, then > experiments, then periods. For example: > > sample=1 period=0 cycle=123 experiment=1 > sample=1 period=0 cycle=124 experiment=1 > sample=1 period=0 cycle=125 experiment=1 > ... > sample=1 period=0 cycle=123 experiment=2 > sample=1 period=0 cycle=124 experiment=2 > sample=1 period=0 cycle=125 experiment=2 > ... > sample=1 period=1 cycle=123 experiment=1 > sample=1 period=1 cycle=124 experiment=1 > sample=1 period=1 cycle=125 experiment=1 > > The MS2s should therefore be listed after all of the MS1s. MzWiff > behaves differently because it resorts all the scans by retention time > when it opens the file (which makes opening the file slow which is fine > for a converter but not for a viewer like SeeMS when opening the WIFF > directly). This enumeration order might be violating an assumption in > Insilicos Viewer. SeeMS may work better in this case (after it loads all > the scan metadata you can sort the scan table by retention time or cycle > just by clicking on that column). It shouldn't make any difference at > all to identification software unless it uses the MS1s and even then > only if it makes an assumption about the way the scans are ordered in > the file. > > -Matt > > Bernt wrote: > > Hi Matt, > > > Thanks for the info. It worked once i copied those DLLs to the > >msconvertdir. > > > Another question: doesmsconverttake out all MS2 scans from wiff > > files? I converted without any filtering, and checked the mzXML file > > with InSilicos Viewer, but couldn't find MS2 scans at all. The > > consecutive scans appear to be MS1 data. > > > Bernt > > > On Sep 23, 11:15 pm, Matthew Chambers > > <[email protected]> wrote: > > >> Did you install it to the default location? If not, you'll have to copy > >> these DLLs to themsconvertdirectory manually: > >> ABSciex.DataAccess.WiffFileDataReader.dll > >> Clearcore.dll > >> ClearCore.Storage.dll > >> rscoree.dll > > >> -Matt > > >> Berntwrote: > > >>> Hi Matt, > > >>> I have just installed the trial version and already activated it and > >>> rebooted the PC. But runningmsconvertstill gives me the message > >>> "[WiffFile::ctor] Reading ABI Wiff files requires Protein pilot 3.0 to > >>> be installed. A trial version ......" > > >>> The wiff files were acquired on a QSTAR and I still have Analyst 1.1 > >>> installed on the PC. Any idea what's wrong? > > >>> Bernt --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
