Hi Matt, Thanks again for your insight.
I ran the command 'msconvert my_fullscan.wiff' in the directory pwiz- bin-windows-x86-vc90-release-2_1_2465 and here is the complete error msg. [Reader_ABI::ctor] Reading ABI WIFF files requires Protein Pilot 3.0 to be installed. A trial version is available for download at: https://licensing.appliedbiosystems.com/download/ProteinPilot/3.0 Error processing file my_fullscan.wiff I got the same error msg when running the same command in the tpp-bin directory. Now I have both Protein Pilot 4.0 and Skyline 0.7.0.2342 installed on my Windows XP. But the error msg remains unchanged. (The web installation of Skyline was successful. But it looked bizzare when I fired it up. It displayed no tool bar whatsoever. The only thing displayed were several dots followed by a small gray box. Something must be wrong either with the build or my system, which is Windows XP Professional Version 2002, Service Pack 2) Thanks for your time, Bob On Jan 18, 10:36 am, Matthew Chambers <[email protected]> wrote: > It sounds like you got the newest pwiz but you're executing an older version > (perhaps the one you > got with TPP). The latest error message should be: > [Reader_ABI::ctor] Reading ABI WIFF files requires Protein Pilot 3.0 or > Skyline to be installed. > Skyline is freely available > at:\nhttps://brendanx-uw1.gs.washington.edu/labkey/project/home/software/S... > > So it points you at Skyline, which is still available. It should work > seamlessly once Skyline is > installed (please let me know if it doesn't). > > -Matt > > On 1/17/2011 5:42 PM, bobxiong wrote: > > > > > Hi Matt, > > > Thanks for your reply and suggestion. > > > I downloaded pwiz-bin-windows-x86-vc90-release-2_1_2467.tar.bz2 to get > > msconvert. However, when I ran the command 'msconvert > > my_fullscan.wiff' on the command line, I got the error msg '... > > requires Protein Pilot 3.0...'. Unfortunately, Protein Pilot 3.0 > > (trial version) doesn't seem to be available from ABI's download > > portal. (part # 1036426 listed on ABI's website but nothing matches > > it). So I probably need an alternate solution. Can you give me another > > pointer? > > > Thanks, > > > Bob > > > On Jan 17, 2:26 pm, Matthew Chambers<[email protected]> > > wrote: > >> I don't know why mzWiff isn't writing a peaks element, but msconvert will. > > >> -Matt > > >> On 1/17/2011 11:29 AM, bobxiong wrote: > > >>> I'm using TPP v4.4 VUVUZELA rev 1, Build 201010121551 (MinGW) to > >>> convert wiff raw data to mzXML. The command executed in TPP was > > >>> c:\Inetpub\tpp-bin\mzWiff -v --mzXML -c1 -g -G --Analyst c:/Inetpub/ > >>> wwwroot/ISB/data/my_fullscan.wiff. > > >>> An excerpt of the output is shown below: > > >>> <scan num="1" > >>> msLevel="1" > >>> peaksCount="140" > >>> polarity="+" > >>> scanType="Q1 Scan" > >>> retentionTime="PT0.001S" > >>> lowMz="106.7" > >>> highMz="1206.8" > >>> basePeakMz="115.9" > >>> basePeakIntensity="3.24903e+006" > >>> totIonCurrent="3.06962e+007"> > >>> </scan> > > >>> I wonder if I could use some sort of advanced option (that I'm not > >>> aware of) to extract info (mz, intensity and retention time) for ALL > >>> the peaks contained in the wiff file rather than for the base peak > >>> only (shown above). If this is not feasible using mzWiff, are there > >>> other tools available to do what I needed? Any advice would be greatly > >>> appreciated. > > >>> Bob- Hide quoted text - > > >> - Show quoted text -- Hide quoted text - > > - Show quoted text - -- 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.
