Msconvert should 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 > msconvert dir. > > Another question: does msconvert take 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 the msconvert directory 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 running msconvert still 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 -~----------~----~----~----~------~----~------~--~---
