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 > > > On Sep 11, 10:20 am, Matt Chambers <[email protected]> > > wrote: > > >> Were all thewifffiles acquired with the same version of Analyst? If > >> not, that's probably the issue. > > >> I recommend trying msconvert which reads WIFFs with a different API from > >> mzWiff: instead of depending on the myriad of different Analyst > >> versions, it uses the unified DLLs from Protein Pilot 3.0 (free trial > >> version available). I've yet to find a non-corruptWIFFfile it doesn't > >> work on. > > >>http://sourceforge.net/projects/proteowizard/files/proteowizard/1.6.0... > > >> -Matt > > >> Sunghyouk Park wrote: > > >>> Thanks for the information. > > >>> The real problem is that a single computer generates working-mzXML > >>> files for somewifffiles but not-working files for otherwifffiles. > >>> (not only on different computers). > >>> For the empty scans, the working-mzxml file generated on a different > >>> computer (for the samewifffile) does have a non-zero peaksCount and > >>> proper information for the particular scan. > > >>> I want to import this mzXML file into mzmine but it reports errors for > >>> the "corrupt peak" and refuses the import. > > >>> Any suggestions will be appreciated. > > >>> Sunghyouk > > >>> On Fri, Sep 11, 2009 at 2:53 AM, Natalie Tasman > >>> <[email protected] <mailto:[email protected]>> > >>> wrote: > > >>> And by the way, the "AAAAAAAAAAA" string that you see is just the > >>> encoding for an empty scan (as you've already seen, peaksCount > >>> will be "0" for these scans.) > > >>> On Sep 10, 2009, at 10:45 AM, Brian Pratt wrote: > > >>>> I expect you'll find the difference between those computers is > >>>> that they have different (or no) versions of the mass spec > >>>> vendor's software installed. The mzwiff program depends on the > >>>> vendors DLLs to read their secret file format, and probably wants > >>>> to see a certain version of that DLL. > > >>>> On Thu, Sep 10, 2009 at 6:10 AM, Sunghyouk <[email protected] > >>>> <mailto:[email protected]>> wrote: > > >>>> Dear mzwiff users > > >>>> I was trying to convert ABI4000 *.wiffformat file to mzXML using > >>>> standalone mzwiff (v. 4.3.1). > >>>> Strangely, it works for some files, but not for others. > >>>> For the exactly same file, it gives working and not-working mzXML > >>>> output files in different computers. > >>>> The problem I found so far is that the not-working mzXML file > >>>> has the > >>>> following: > >>>> In just a few scans out of thousands, some scan has > >>>> "AAAAAAAAAAA" in > >>>> the <peaks></peaks> block > >>>> as shown below (right above the </scan> tag below) > > >>>> <scan num="2857" > >>>> msLevel="1" > >>>> peaksCount="0" > >>>> polarity="+" > >>>> scanType="Q1 Scan" > >>>> retentionTime="PT1728.74S" > >>>> lowMz="0" > >>>> highMz="0" > >>>> basePeakMz="0" > >>>> basePeakIntensity="0" > >>>> totIonCurrent="0" > > >>>> <peaks precision="32" > >>>> byteOrder="network" > >>>> contentType="m/z-int" > >>>> compressionType="none" > >>>> compressedLen="0" >AAAAAAAAAAA=</peaks> > >>>> </scan> > > >>>> In addition, most of the parameters are set to "0" > >>>> (peaksCount, lowMz, > >>>> etc) > > >>>> Does anyone know how to fix this problem? > > >>>> Thanks. --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
